Compositions and methods for treating or preventing prostate cancer and for detecting androgen receptor variants

ABSTRACT

The invention features diagnostic and therapeutic methods and compositions featuring androgen receptor variant proteins and nucleic acid molecules whose expression is increased in androgen related diseases or disorders.

RELATED APPLICATIONS/PATENTS & INCORPORATION BY REFERENCE

This application is a continuation of and claims priority to U.S. patentapplication Ser. No. 12/988,299, filed on Oct. 15, 2010, which is aNational Stage Application of PCT/US2009/02392, filed on Apr. 16, 2009,which claims the benefit of U.S. Provisional Application No. 61/124,328,filed on Apr. 16, 2008 and U.S. Provisional Application No. 61/114,153,filed on Nov. 13, 2008. The entire contents of the aforementionedapplications are hereby incorporated by reference.

Each of the applications and patents cited in this text, as well as eachdocument or reference cited in each of the applications and patents(including during the prosecution of each issued patent; “applicationcited documents”), and each of the PCT and foreign applications orpatents corresponding to and/or claiming priority from any of theseapplications and patents, and each of the documents cited or referencedin each of the application cited documents, are hereby expresslyincorporated herein by reference. More generally, documents orreferences are cited in this text, either in a Reference List before theclaims, or in the text itself; and, each of these documents orreferences (“herein-cited references”), as well as each document orreference cited in each of the herein-cited references (including anymanufacturer's specifications, instructions, etc.), is hereby expresslyincorporated herein by reference.

SEQUENCE LISTING

The present application contains a sequence listing that has beensubmitted in ASCII format via EFS-Web on Aug. 3, 2015, containing thefile name SL 36406.0009 U2-, which is 40,635 bytes in size, created onJul. 23, 2015, comprises 47 sequences, and is herein incorporated byreference in its entirety.

BACKGROUND OF THE INVENTION

Prostate cancer (PCa) depends on androgenic signaling for growth andsurvival. Androgens exert their cellular and physiologic effects throughbinding to the androgen receptor (AR), a member of the steroid hormonereceptor family of transcription factors. The human AR gene is locatedon chromosome Xq11-12 and spans approximately 180 kb of DNA with eightknown exons. The prototype AR protein contains several functionaldomains. The NH2-terminal domain (NTD), encoded by exon 1, constitutesapproximately 60% of the 110-kDa full-length protein and is thetranscriptional regulatory region of the protein. The centralDNA-binding domain (DBD) is encoded by exons 2 and 3, whereas exons 4 to8 code for the COOH-terminal ligand-binding domain (LBD). Androgenbinding to the AR LBD allows entry of the ligand-bound receptor into thenucleus and subsequent transcriptional regulation of androgen-responsivegenes.

Hormonal therapy has been used since 1941 for the treatment ofmetastatic prostate cancer. Hormone deprivation therapies employingsurgical and/or medical castration as well as their combination withanti-androgens have since become the mainstay of systemic treatment foradvanced prostate cancer. Hormonal therapies for advanced PCa targetAR-mediated functions by suppressing the production of androgens and/orandrogen binding to the AR LBD. Although these therapies often result ina period of clinical regression, they are not curative due toprogression to hormone-refractory PCa (HRPC) for which effectivetherapeutic options are limited. In a contemporary clinical setting, thelength of clinical remission, often assessed by serum prostate-specificantigen (PSA) measurements, varies substantially due to a wide spectrumof clinical phenotypes among treated patients. Almost invariably,however, prostate cancer develops castration-resistant phenotype andprogresses to a life-threatening stage, despite hormone therapies. Thewidespread use of hormone deprivation therapies is manifested in theobservation that almost all patients who die from prostate cancer hadreceived and failed hormone-deprivation therapies.

A few lines of evidence have established that, unlike human breastcancer, prostate cancer progression upon hormone therapy is not due toloss of dependence on hormonal signaling but, instead, characterized bysustained androgenic signaling that bypasses the requirement forphysiological levels of androgens. First, with only certain exceptions,prostate cancer patients dying from castration-resistant prostate cancerhave very high levels of serum PSA, the production of which is driven byandrogenic signaling. Second, castration-resistant prostate cancers haveelevated expression levels of the key mediator of androgenic signaling,the AR, and this is a very consistent molecular feature in tissuesderived from patients with castration-resistant prostate cancer. Third,a subset of prostate cancers that relapsed following hormone therapycontinue to respond to second-line hormone therapies designed to disruptthe AR signaling axis, suggesting that AR-mediated androgenic signalingis still operating among these tumors. While it is possible thatAR-negative prostate cancer cells may give rise to androgen-independentprostate carcinoma, prostate tumors comprised of mainly AR-negativemalignant cells (i.e., small cells and neuroendocrine cells) are rare.

AR-mediated functions are not completely abrogated by the existinghormone therapies. HRPC continues to depend on AR-mediated functions butbypasses the requirement for physiologic levels of androgens. Molecularalterations involving AR itself, such as AR overexpression andgain-of-function AR LBD mutations, are common in HRPC and allow forcontinued AR-mediated genomic functions under the presence of reduced oraltered ligands. Despite the established clinical relevance of thesewell-characterized AR alterations in HRPC, only a few previous studieshave suggested an alternative mechanism for HRPC and investigated theputative role of AR variants lacking the AR LBD.

Accordingly, a need remains to for more effective compositions andmethods for the treatment of prostate cancer.

SUMMARY OF THE INVENTION

Included in the present invention are a number of novel AR variants.These novel AR variants are encoded by spliced transcripts and do nothave the protein domains needed to bind to androgens but areconstitutively active and drive AR signaling in the complete absence ofandrogens. The present inventors have performed a comprehensive insilico sequence analysis and tiling expression microarray analysis ofthe human AR genomic locus and uncovered multiple novel ARDLBD variantswith intact coding potential for the full AR NTD and AR DBD. The presentinventors have shown that an antibody generated against one of the ARvariants detects AR variant protein frequently in HRPC specimens.Accordingly, the expression pattern and the validatedandrogen-independent function of these newly identified AR variantscontribute a new understanding to the molecular mechanism of HRPC thatwill affect the overall management of patients with advanced PCa.

In one aspect, the invention features a method of determining if asubject will respond to androgen therapy, the method comprisingdetermining the level of expression or biological activity of anandrogen receptor variant polypeptide in a subject sample wherein analteration in the level of expression or biological activity relative tothe expression or biological activity in a reference indicates that thesubject will respond to androgen therapy.

In another aspect, the invention features a method of determining if asubject will respond to androgen therapy, the method comprisingdetermining the level of expression or biological activity of anandrogen receptor variant nucleic acid in a subject sample wherein analteration in the level of expression relative to the expression in areference indicates that the subject will respond to androgen therapy.

In one embodiment, the subject is has or has a propensity to developprostate cancer.

In one aspect, the present invention provides a method of diagnosing asubject as having, or having a propensity to develop prostate cancer,the method comprising determining the level of expression of an androgenreceptor variant nucleic acid in a subject sample wherein an alterationin the level of expression relative to the expression in a referenceindicates that the subject has or has a propensity to develop anandrogen related disease or disorder. In one aspect, the presentinvention provides a method of diagnosing a subject as having, or havinga propensity to develop prostate cancer, the method comprisingdetermining the level of expression or biological activity of anandrogen receptor variant polypeptide in a subject sample wherein analteration in the level of expression or biological activity relative tothe expression or biological activity in a reference indicates that thesubject has or has a propensity to develop an androgen related diseaseor disorder.

In another aspect, the invention provides a method of determining therisk of recurrence of prostate cancer, the method comprising determiningthe level of expression of an androgen receptor variant nucleic acidmolecule in a subject sample, wherein an increased level of expressionrelative to a reference indicates that the subject has an increased riskof recurrence of an androgen related disease or disorder.

In still another aspect, the invention provides a method of determiningthe risk of recurrence of prostate cancer in a subject, the methodcomprising determining the level of expression or activity of anandrogen receptor variant polypeptide in a subject sample, wherein anincreased level of expression or activity relative to the level ofexpression or activity in a reference indicates that the subject has anincreased risk of recurrence of an androgen related disease or disorder.

In another aspect, the invention provides a method of monitoring asubject diagnosed as having prostate cancer, the method comprisingdetermining the expression of an androgen receptor variant nucleic acidmolecule in a subject sample, wherein an alteration in the level ofexpression relative to the level of expression in a reference indicatesthe severity of the disease or disorder in the subject.

In still another aspect, the invention provides a method of monitoring asubject diagnosed as having prostate cancer, the method comprisingdetermining the level of expression or activity of an androgen receptorvariant polypeptide in a subject sample, wherein an alteration in thelevel of expression or activity relative to the level of activity in areference indicates the severity of the androgen related disease ordisorder in the subject.

In another aspect, the invention provides a method of determining theprogression of prostate cancer in a subject, the method comprisingdetermining the expression of an androgen receptor variant nucleic acidmolecule in a subject sample, wherein an alteration in the level ofexpression relative to the level of expression in a reference indicatesthe progression of the disease or disorder in the subject.

In another aspect, the invention provides a method of diagnosing asubject as having, or having a propensity to develop, an androgenrelated disease or disorder, the method comprising determining the levelof expression of an androgen receptor variant nucleic acid molecule in asubject sample, wherein an increased level of expression relative to areference indicates that the subject has or has a propensity to developan androgen related disease or disorder.

In still another aspect, the invention provides a method of diagnosing asubject as having, or having a propensity to develop, an androgenrelated disease or disorder, the method comprising determining the levelof expression of an androgen receptor variant polypeptide in a subjectsample, wherein an increased level of expression relative to the levelof expression in a reference indicates that the subject has or has apropensity to develop an androgen related disease or disorder.

In one embodiment of any one of the above aspects, the level ofexpression is determined in an immunological assay.

In one embodiment of any one of the methods described herein, the methodis used to determine if a subject will be responsive to androgentherapy.

In another embodiment of any one of the above aspects, the subject isbeing treated for an androgen related disease or disorder.

In another embodiment of any one of the above aspects, the alteration isan increase. In a related embodiment, the increase corresponds to afailure to respond to androgen therapy.

In another embodiment of any one of the above aspects, the reference isa control subject sample.

In another embodiment of any one of the above aspects, the reference isa subject sample obtained at an earlier time point.

In yet another embodiment of any one of the above aspects, the referenceis a subject sample obtained before surgical treatment.

In another embodiment, the reference is the level of androgen receptorvariant polypeptide or nucleic acid molecule present in a control sampleobtained from subjects with a disease of a lesser severity. In a relatedembodiment, the disease of lesser severity is an early stagenon-aggressive prostate cancer.

In another embodiment of any one of the above aspects, the subjectsample is a biological sample.

In another embodiment of any one of the above aspects, the method isused to diagnose a subject as having prostate cancer.

In another embodiment of any one of the above aspects, the method isused to determine the treatment regimen for a subject having prostatecancer.

In another embodiment of any one of the above aspects, the method isused to monitor the condition of a subject being treated for prostatecancer.

In another embodiment of any one of the above aspects, the method isused to determine the prognosis of a subject having prostate cancer. Instill another embodiment of any one of the above aspects, the method isused to determine the prognosis of a subject following androgen therapy.In a related embodiment, a poor prognosis determines an aggressivetreatment regimen for the subject.

In another embodiment of any one of the above aspects, the methodfurther comprises obtaining a biological sample from the subject.

In another related embodiment, the androgen related disease or disorderis selected from the group consisting of: prostate cancer, androgenicalopecia, infertility, irregular menstrual periods, excessive hairgrowth, acne, obesity, insulin resistance, and polycystic ovariansyndrome.

In a further embodiment, the androgen related disease or disorder isprostate cancer.

In another embodiment of any one of the above aspects, the prostatecancer is hormone refractory prostate cancer.

In another embodiment of any one of the above aspects, the prostatecancer is hormone naïve prostate cancer.

In another embodiment of any one of the above aspects, the expression ofan androgen receptor variant nucleic acid molecule detected using ahybridization reaction comprising hybridizing the sample to one or moreprimer sets.

In one embodiment, the hybridization reaction is a polymerase chainreaction. In another embodiment, each primer set comprises a forwardprimer and a reverse primer, wherein the forward primer is complementaryto a nucleic acid sequence corresponding to a nucleic acid sequenceselected from SEQ ID NOs 1-7, or SEQ ID NO: 39 or fragments thereof, andthe reverse primer is reverse complementary to a nucleic acid sequencecorresponding to a nucleic acid sequence selected from SEQ ID NOs 1-7 orSEQ ID NO: 39.

In a related embodiment, the primer set is selected from the groupconsisting of: (P1): TGTCACTATGGAGCTCTCACATGTGG (SEQ ID NO: 15) andCACCTCTCAAATATGCTAGACGAATCTGT (SEQ ID NO: 16); (P2)TGTCACTATGGAGCTCTCACATGTGG (SEQ ID NO: 17) andGTACTCATTCAAGTATCAGATATGCGGTATCAT (SEQ ID NO: 18); (P3)TGTCACTATGGAGCTCTCACATGTGG (SEQ ID NO: 19) andCTGTGGATCAGCTACTACCTTCAGCTC (SEQ ID NO: 20); (P4)GTTGCTCCCGCAAGTTTCCTTCTC (SEQ ID NO: 21) and CTGTTGTGGATGAGCAGCTGAGAGTCT(SEQ ID NO: 22); (P5) GTTGCTCCCGCAAGTTTCCTTCTC (SEQ ID NO: 23) andTTTGAATGAGGCAAGTCAGCCTTTCT (SEQ ID NO: 24); (P6)CCATCTTGTCGTCTTCGGAAATGT TATGAAGC (SEQ ID NO: 25) andCTGTTGTGGATGAGCAGCTGAGAGTCT (SEQ ID NO: 26); (P7)CCATCTTGTCGTCTTCGGAAATGTT ATGAAGC (SEQ ID NO: 27) andTTTGAATGAGGCAAGTCAGCCTTTCT (SEQ ID NO: 28); (P8) CCATCTTGTCGTCTTCGGAAATGTTATGAAGC (SEQ ID NO: 29) and AGCTTCTGGGTTGTCTCCTCAGTGG (SEQ ID NO: 30);(P9)-Tgtcactatggagctctcacatgtgg (SEQ ID NO: 37) andCattgtggccaacatgacacttca (SEQ ID NO: 38).

In another aspect, the invention features a method for identifying asubject as having or having a propensity to develop prostate cancer, themethod comprising detecting an alteration in the sequence of an androgenreceptor nucleic acid molecule relative to the sequence or expression ofa reference molecule.

In one embodiment, the alteration is detected using a hybridizationreaction comprising hybridizing the sample to one or more primer sets.In a related embodiment, the hybridization reaction is a polymerasechain reaction. In a further related embodiment, the primer sets areselected from the group consisting of: (P1): TGTCACTATGGAGCTCTCACATGTGG(SEQ ID NO: 15) and CACCTCTCAAATATGCTAGACGAATCTGT (SEQ ID NO: 16); (P2)TGTCACTATGGAGCTCTCACATGTGG (SEQ ID NO: 17) andGTACTCATTCAAGTATCAGATATGCGGTATCAT (SEQ ID NO: 18); (P3)TGTCACTATGGAGCTCTCACATGTGG (SEQ ID NO: 19) andCTGTGGATCAGCTACTACCTTCAGCTC (SEQ ID NO: 20); (P4)GTTGCTCCCGCAAGTTTCCTTCTC (SEQ ID NO: 21) and CTGTTGTGGATGAGCAGCTGAGAGTCT(SEQ ID NO: 22); (P5) GTTGCTCCCGCAAGTTTCCTTCTC (SEQ ID NO: 23) andTTTGAATGAGGCAAGTCAGCCTTTCT (SEQ ID NO: 24); (P6)CCATCTTGTCGTCTTCGGAAATGT TATGAAGC (SEQ ID NO: 25) andCTGTTGTGGATGAGCAGCTGAGAGTCT (SEQ ID NO: 26); (P7)CCATCTTGTCGTCTTCGGAAATGTT ATGAAGC (SEQ ID NO: 27) andTTTGAATGAGGCAAGTCAGCCTTTCT (SEQ ID NO: 28); (P8) CCATCTTGTCGTCTTCGGAAATGTTATGAAGC (SEQ ID NO: 29) and AGCTTCTGGGTTGTCTCCTCAGTGG (SEQ ID NO: 30);(P9) Tgtcactatggagctctcacatgtgg (SEQ ID NO: 37) andCattgtggccaacatgacacttca (SEQ ID NO: 38).

In another aspect, the invention features an androgen receptor variantantibody that specifically binds to an androgen receptor variant (AR-V)protein or fragment thereof.

In one embodiment, the antibody specifically binds to an androgenreceptor variant-7 (AR-V7) protein.

In one embodiment, the antibody specifically binds to an androgenreceptor variant-8 (AR-V8) protein.

In another embodiment, the antibody specifically binds to an androgenreceptor variant-1 (AR-V 1) protein.

In still another further embodiment, the antibody binds to a CKHLKMRPepitope of an AR-V polypeptide, corresponding to SEQ ID NO: 33.

In another embodiment of any one of the above aspects, the antibody ismonoclonal.

In another aspect, the invention features a polypeptide comprising anisolated androgen receptor protein variant, or fragment thereof, havingsubstantial identity to androgen receptor variant 1, 2, 3, 4, 5, 6, 7 or8 (AR-V1-AR-V8), wherein the variant is upregulated in prostate cancer.

In one embodiment, the androgen receptor protein variant is at least 85%identical to androgen receptor variant 1, 2, 3, 4, 5, 6, 7 or 8.

In another embodiment, the androgen receptor protein variant comprisesat least the androgen receptor NH2 terminal domain (NTD) and DNA bindingdomain (DBD).

In another related embodiment, the polypeptide is linked to a detectableamino acid sequence.

In still another related embodiment, the polypeptide is linked to anaffinity tag.

In another embodiment of the above aspects, the nucleic acid moleculeencodes a polypeptide of any one of the above.

In another embodiment, the invention features a vector comprising thenucleic acid molecule of any one of the above aspects.

In another aspect, the invention features an isolated androgen receptorvariant inhibitory nucleic acid molecule, wherein the inhibitory nucleicacid molecule specifically binds at least a fragment of a nucleic acidmolecule encoding an androgen receptor variant protein.

In one embodiment, the vector comprises a nucleic acid molecule encodingthe nucleic acid molecule of the above aspects.

In another embodiment, the vector is an expression vector.

In still another embodiment, the nucleic acid molecule is operablylinked to a promoter.

In still another embodiment, the promoter is suitable for expression ina mammalian cell.

In another embodiment, the invention features a host cell comprising anucleic acid molecule of any one of the above aspects.

In one embodiment, the cell expresses an androgen receptor variantprotein.

In another embodiment, the cell is in vitro. In another embodiment, thecell is in vivo.

In still another embodiment, the cell is a mammalian cell. In stillanother embodiment, the cell is a human cell.

In another aspect, the invention features a double-stranded RNAcorresponding to at least a portion of an androgen receptor variantnucleic acid molecule that encodes an androgen receptor variant protein,wherein the double-stranded RNA is capable of altering the level ofprotein encoded by the androgen receptor variant nucleic acid molecule.

In one embodiment, the RNA is an siRNA.

In another aspect, the invention features an antisense nucleic acidmolecule, wherein the antisense nucleic acid molecule is complementaryto an androgen receptor variant nucleic acid molecule that encodes anandrogen receptor variant protein, and wherein the antisense is capableof altering expression from the nucleic acid molecule to which it iscomplementary.

In another aspect, the invention features a primer capable of binding toan androgen receptor variant nucleic acid molecule encoding an androgenreceptor variant protein variant.

In one embodiment, the primer is capable of binding to an androgenreceptor variant nucleic acid molecule, wherein the primer is selectedfrom the group consisting of: (SEQ ID NO: 15), (SEQ ID NO: 16), (SEQ IDNO: 17), (SEQ ID NO: 18), (SEQ ID NO: 19), (SEQ ID NO: 20), (SEQ ID NO:21), (SEQ ID NO: 22), (SEQ ID NO: 23), (SEQ ID NO: 24), (SEQ ID NO: 25),(SEQ ID NO: 26), (SEQ ID NO: 27), (SEQ ID NO: 28), (SEQ ID NO: 29), (SEQID NO: 30), (SEQ ID NO: 37) and (SEQ ID NO: 38).

In another aspect, the invention features an androgen receptor biomarkerpurified on a biochip.

In another aspect, the invention features a microarray comprising atleast two nucleic acid molecules, or fragments thereof, fixed to a solidsupport, wherein at least one of the nucleic acid molecules is anandrogen receptor variant nucleic acid molecule.

In another aspect, the invention features a microarray comprising atleast two polypeptides, or fragments thereof, bound to a solid support,wherein at least one of the polypeptides on the support is an androgenreceptor variant polypeptide.

In another aspect, the invention features a kit for the diagnosis ofprostate cancer in a subject comprising a primer set that detects anandrogen receptor variant nucleic acid molecule, or fragment thereof,and written instructions for use of the kit for detection of prostatecancer.

In another aspect the invention features a diagnostic kit for thediagnosis of an androgen related disease or disorder in a subjectcomprising a primer set that detects an androgen receptor variantnucleic acid molecule, or fragment thereof, and written instructions foruse of the kit for detection of an androgen related disease or disorder.

In still another aspect, the invention features a diagnostic kit for thediagnosis of prostate cancer in a subject comprising an antibody thatspecifically binds an androgen receptor variant polypeptide, or fragmentthereof, and written instructions for use of the kit for detection ofprostate cancer.

In another aspect, the invention features a kit identifying a subject ashaving or having a propensity to develop prostate cancer, comprising anadsorbent, wherein the adsorbent retains an androgen receptor variantbiomarker, and written instructions for use of the kit for detection ofprostate cancer.

In another aspect, the invention features a kit for determining if asubject will respond to androgen therapy, the kit comprising a primerset to detect an androgen receptor variant nucleic acid molecule, orfragment thereof, and written instructions for use of the kit fordetermining if a subject will respond to androgen therapy.

In still another aspect, the invention features a kit for determining ifa subject will respond to androgen therapy, the kit comprising anantibody that specifically binds an androgen receptor variantpolypeptide, or fragment thereof, and written instructions for use ofthe kit for determining if a subject will respond to androgen therapy.

In another aspect, the invention features a method of altering theexpression of an androgen receptor variant nucleic acid molecule in acell, the method comprising contacting the cell with an effective amountof a compound capable of altering the expression of the androgenreceptor variant nucleic acid molecule.

In one embodiment, the compound is an antisense nucleic acid molecule, asmall interfering RNA (siRNA), or a double stranded RNA (dsRNA) thatinhibits the expression of an androgen receptor variant nucleic acidmolecule.

In one aspect, the invention features a method of altering androgenreceptor variant protein expression in a cell, the method comprisingcontacting the cell with a compound capable of altering the expressionof an androgen receptor variant polypeptide.

In another aspect, the invention features a method of treating orpreventing prostate cancer, the method comprising administering to asubject in need thereof an effective amount of a pharmaceuticalcomposition that alters expression of an androgen receptor variantpolypeptide.

In still another aspect, the invention features a method of identifyinga compound that inhibits prostate cancer the method comprisingcontacting a cell that expresses an androgen receptor variant nucleicacid molecule with a candidate compound, and comparing the level ofexpression of the nucleic acid molecule in the cell contacted by thecandidate compound with the level of expression in a control cell notcontacted by the candidate compound, wherein an alteration in expressionof the androgen receptor variant nucleic acid molecule identifies thecandidate compound as a compound that inhibits prostate cancer.

In one embodiment, the alteration in expression is a decrease intranscription.

In another embodiment, the alteration in expression is a decrease intranslation.

Aspect, the invention features a method of identifying a compound thatinhibits prostate cancer, the method comprising contacting a cell thatexpresses an androgen receptor variant polypeptide with a candidatecompound, and comparing the level of expression of the polypeptide inthe cell contacted by the candidate compound with the level ofpolypeptide expression in a control cell not contacted by the candidatecompound, wherein an alteration in the expression of the androgenreceptor variant polypeptide identifies the candidate compound as acompound that inhibits prostate cancer.

In still another aspect, the invention features a method of identifyinga compound that inhibits prostate cancer, the method comprisingcontacting a cell that expresses an androgen receptor variantpolypeptide with a candidate compound, and comparing the biologicalactivity of the polypeptide in the cell contacted by the candidatecompound with the level of biological activity in a control cell notcontacted by the candidate compound, wherein an alteration in thebiological activity of the androgen receptor variant polypeptideidentifies the candidate compound as a candidate compound that inhibitsprostate cancer.

In one embodiment of the above aspects, the cell is a human cell. Inanother embodiment of the above aspects, the cell is a neoplastic cell.

In another embodiment of the above aspects, the cell is in vitro. Inanother embodiment of the above aspects, the cell is in vivo.

In still another embodiment of the above aspects, the alteration inexpression is assayed using an immunological assay, an enzymatic assay,or a radioimmunoassay.

In one embodiment, the androgen receptor variant polypeptide comprises asequence selected from the group consisting of: SEQ ID NO: 8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ IDNO: 14, and SEQ ID NO: 40 or fragments thereof.

In one embodiment of any one of the above aspects, the androgen receptorvariant polypeptide comprises SEQ ID NO: 8, or a fragment thereof. Instill another embodiment, the androgen receptor variant polypeptidecomprises SEQ ID NO: 9, or a fragment thereof. In still anotherembodiment, the androgen receptor variant polypeptide comprises SEQ IDNO: 40, or a fragment thereof.

In one embodiment of any one of the above aspects, the androgen receptorvariant nucleic acid comprises a sequence selected from the groupconsisting of: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4,SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 39 or fragmentsthereof.

In another embodiment, the androgen receptor variant nucleic acidcomprises SEQ ID NO: 1, or a fragment thereof. In still anotherembodiment, the androgen receptor variant nucleic acid comprises SEQ IDNO: 2. In still another embodiment, the androgen receptor variantnucleic acid comprises SEQ ID NO: 39.

In another embodiment of any one of the above aspects, the prostatecancer is hormone refractory prostate cancer. In another embodiment ofany one of the above aspects, the prostate cancer is hormone naiveprostate cancer.

In another embodiment of any one of the above aspects, SEQ ID NO: 1-SEQID NO: 7 and SEQ ID NO: 39 can correspond to a nucleic acid sequence, orfragment thereof, and SEQ ID NO: 8-SEQ ID NO: 15 and SEQ ID NO: 40 cancorrespond to an amino acid sequence, or fragment thereof, as follows:

SEQ ID NO: 1 TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTCTTCTTCAAAAGAGCCGCTGAAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGG GATGACTCTGGGA

AAAAATTCCGGGTTGGCAATTGCAAGCATCTCAAAATGACCAGACCCTGAAGAAAGGCTGACTTGCCTCATTCAAAATGAGGGCTCTAGAGGGCTCTAGTGGATAGTCTGGAGAAACCTGGCGTCTGAGGCTTAGGAGCTTAGGTTTTTGCTCCTCAACACAGACTTTGACGTTGGGGTTGGGGGCTACTCTCTTGATTGCTGACTCCCTCCAGCGGGACCAATAGTGTTTTCCTACCTCACAGGGATGTTGTGAGGACGGGCTGTAGAAGTAATAGTGGTTACCACTCATGTAGTTGTGAGTATCATGATTATTGTTTCCTGTAATGTGGCTTGGCATTGGCAAAGTGCTTTTTGATTGTTCTTGATCACATATGATGGGGGCCAGGCACTGACTCAGGCGGATGCAGTGAAGCTCTGGCTCAGTCGCTTGCTITICGTGGTGTGCTGCCAGGAAGAAACTTTGCTGATGGGACTCAAGGTGTCACCTTGGACAAGAAGCAACTGTGTCTGTCTGAGGTTCCTGTGGCCATCTTTATTTGTGTATTAGGCAATTCGTATTTCCCCCTTAGGTTCTAGCCTTCTGGATCCCAGCCAGTGACCTAGATCTTAGCCTCAGGCCCTGTCACTGAGCTGAAGGTAGTAGCTGATCCACAGAAGTTCAGTAAACAAGGACCAGATTTCTGCTTCTCCAGGAGAAGAAGCCAGCCAACCCCTCTCTTCAAACACACTGAGAGACTACAGTCCGACTTTCCCTCTTACATCTAGCCTTACTGTAGCCACACTCCTTGATTGCTCTCTCACATCACATGCTTCTCTTCATCAGTTGTAAGCCTCTCATTCTTCTCCCAAGCCAGACTCAAATATTGTATTGATGTCAAAGAAGAATCACTTAGAGTTTGGAATATCTTGTTCTCTCTCGCTCCATAGCTTCCATATTGACACCAGTTTCTTTCTAGTGGAGAAGTGGAGTCTGTGAAGCCAGGGAAACACACATGTGAGAGTCAGAAGGACTCTCCC SEQ ID NO: 2TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTC′TTCTTCAAAAGAGCCGCTGAAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGG GATGACTCTGGGA

CTGTTGTTGTTTCTGAAAGAATCTTGAGGGTGTTTGGAGTCTCAGAATGGCTTCCTTAAAGACTACCTTCAGACTCTCAGCTGCTCATCCACAACAGAGATCAGCCTTTCTTTGTAGATGATTCATTCCTGGCTGCATTTGAAAACCACATATTGTTAATTGCTTGACGAATTTAAATCCCTTGACTACTTTTCATTTCAGAAAACACTTACAAAAAAAGTCCAAATGAGGACCTTCCCTCCAGTGAATTAGCTGTGGCTTTCTCACAGTCCATAGTTAGGATAAATGTAAAGCCATTTCTCATTTTTCTCCGCACTTTCCAAGGGTACACTCCTTGTTTCCAAGATGGAATGAGAAATAAAGAAGTGCCCTTCCTGCCATCTTCTCCCCTGACCCTTTCCTCCTTCCCACTTTCCTCCTATTCCTCCCCAAACATGATTTATTTCTGCGTTTTGCAACTCTTGAGTTCTCAGCATTTAGTAAATGGTGTTGGTCCCTGTTGATTCCTTCCTCTCCTGGACCATGGAAGGTAGTAGGCCTTTCAGAAATTTCAGGTAGCAGCCAAACCCCAGAAGAAGAGAAGGAACACAGAGACCTAGACCATGTGAGAACCTGAGGTGTGCAGCATTTACTTCACAGATTCGTCTAGC ATATTTGAGAGGTGSEQ ID NO: 3 TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTCTTCTTCAAAAGAGCCGCTGAAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGA

CTGTTGTTGTTTCTGAAAGAATCTTGAGGGTGTTTGGAGTCTCAGAATGGCTTCCTTAAAGACTACCTTCAGACTCTCAGCTGCTCATCCACAACAGAGATCAGCC TTTCTTTGTAGATGATTCATTCCTGGCTGCATTTGAAAACCACATATTGTTAATTGCTTGACGAATTTAAATCCCTTGACTACTTTTCATTTCAGAAAACACTTACAAAAAAAGTCCAAATGAGGACCTTCCCTCCAGTGAATTAGCTGTGGCTTTCTCACAGTCCATAGTTAGGATAAATGTAAAGCCATTTCTCATTTTTCTCCGCACTTTCCAAGGGTACACTCCTTGTTTCCAAGATGGAATGAGAAATAAAGAAGTGCCCTTCCTGCCATCTTCTCCCCTGACCCTTTCCTCCTTCCCACTTTCCTCCTATTCCTCCCCAAACATGATTTATTTCTGCGTTTTGCAACTCTTGAGTTCTCAGCATTTAGTAAATGGTGTTGGTCCCTGTTGAT

CCTTCCTCTCCTGGACCATGGAAGGTAGTAGGCCTTTCAGAAATTTCAGGTAGCAGCCAAACCCCAGAAGAAGAGAAGGAACACAGAGACCTAGACCATGTGAGAACCTGAGGTGTGCAGCATTTACTTCACAGATTCGTCTAGCATATTTGAGAGGTG SEQ ID NO: 4TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTCTTCTTCAAAAGAGCCG CTGAA

GATTTTTCAGAATGAACAAATTAAAAGAATCATCAGACACTAACCCCAAGCCATACTGCATGGCAGCACCAATGGGACTGACAGAAAACAACAGAAATAGGAAGAAATCCTACAGAGAAACAAACTTGAAAGCTGTCTCATGGCCTTTGAATCATACTTAAGTTTTATGATGGAAGGATACGACTATGAAGAAAGACACAGAGCAACATCAGACAGTCAAGAATTTCAGAGCCAGCTGGCATGCAGTGGACCTCATGCCAGCCCATTTTATGACTATTTAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGAGCAGCTGTTGTTGTTTCTGAAAGAATCTTGAGGGTGTTTGGAGTCTCAGAATGGCTTCCTTAAAGACTACCTTCAGACTCTCAGCTGCTCATCCACAACAGAGATCAGCCTTTCTTTGTAGATGATTCATTCCTGGCTGCATTTGAAAACCACATATTGTTAATTGCTTGACGAATTTAAATCCCTTGACTACTTTTCATTTCAGAAAACACTTACAAAAAAAGTCCAAATGAGGACCTTCCCTCCAGTGAATTAGCTGTGGCTTTCTCACAGTCCATAGTTAGGATAAATGTAAAGCCATTTCTCATTTTTCTCCGCACTTTCCAAGGGTACACTCCTTGTTTCCAAGATGGAATGAGAAATAAAGAAGTGCCCTTCCTGCCATCTTCTCCCCTGACCCTTTCCTCCTTCCCACTTTCCTCCTATTCCTCCCCAAACATGATTTATTTCTGCGTTTTGCAACTCTTGAGTTCTCAGCATTTAGTAAATGGTGTTGGTCCCTGTTGATTCCTTCCTCTCCTGGACCATGGAAGGTAGTAGGCCTTTCAGAAATTTCAGGTAGCAGCCAAACCCCAGAAGAAGAGAAGGAACACAGAGACCTAGACCATGTGAGAACCTGAGGTGTGCAGCATTTACTTCACAGATTCGTCTAGCATATTTGAGAGGTG SEQ ID NO: 5TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTCTTCTTCAAAAGAGCCGCTGAAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGG GATGACTCTGGGA

GATTTTTCAGAATGAACAAATTAAAAGAATCATCAGACACTAACCCCAAGCCATACTGCATGGCAGCACCAATGGGACTGACAGAAAACAACAGAAATAGGAAGAAATCCTACAGAGAAACAAACTTGAAAGCTGTCTCATGGCCTTTGAATCATACTTAAGTTTTATGATGGAAGGATACGACTATGAAGAAAGACACAGAGCAACATCAGACAGTCAAGAATTTCAGAGCCAGCTGGCATGCAGTGGACCTCATGCCAGCCCATTTTATGACTATTTAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGAGCAGCTGTTGTTGTTTCTGAAAGAATCTTGAGGGTGTTTGGAGTCTCAGAATGGCTTCCTTAAAGACTACCTTCAGACTCTCAGCTGCTCATCCACAACAGAGATCAGCCTTTCTTTGTAGATGATTCATTCCTGGCTGCATTTGAAAACCACATATTGTTAATTGCTTGACGAATTTAAATCCCTTGACTACTTTTCATTTCAGAAAACACTTACAAAAAAAGTCCAAATGAGGACCTTCCCTCCAGTGAATTAGCTGTGGCTTTCTCACAGTCCATAGTTAGGATAAATGTAAAGCCATTTCTCATTTTTCTCCGCACTTTCCAAGGGTACACTCCTTGTTTCCAAGATGGAATGAGAAATAAAGAAGTGCCCTTCCTGCCATCTTCTCCCCTGACCCTTTCCTCCTTCCCACTTTCCTCCTATTCCTCCCCAAACATGATTTATTTCTGCGTTTTGCAACTCTTGAGTTCTCAGCATTTAGTAAATGGTGTTGGTCCCTGTTGAT

CCTTCCTCTCCTGGA CCATGGAAGGTAGTAGGCCTTTCAGAAATTTCAGGTAGCAGCCAAACCCCAGAAGAAGAGAAGGAACACAGAGACCTAGACCATGTGAGAACCTGAGGTGTGCAGCATTTACTTCACAGATTCGTCTAGCATATTTGAGAGGTG SEQ ID NO: 6GGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGAC TCTGGGA

ACTAGAATTCCAAAGACCCTCAGGCTGGTGATGCAAGTGGGAAGTCTCATTTCTGAGAAGTGCTGCTTCCTACCCACAATTCTTTGATAGCTGAGTGCTTTAGCTGATCTGCATAACTGAGGTGTGCACCAAGGAGCAGAATTACTCTATAAATTTTGGCATCAACATGTGCAACTTGTGACTCAGCACTTTGAAACTCTGGGGATTTTTTTGTTTGGTTGGTTTTTGTTTTAAGATGTCCTGTGGTATAGTGGAAATAGTACAATAGACTCAGATACAGAGAGGCCTTGTTTCTAGTCTTGGTTCTGTCACTTACTATCTTGATGTCCTTGCACAAATCACCAGACCTCTCTGAGCCTCAGTTTCTCCAACCACACTGTGGGAATAATAAAATCTTTTTTACGGCATTGTTGTAAGTATGCAGAGAAACTGGTACACAGTAGCCACACAATCAATGTCACCGTACCCTTCAGCCCTTCTTTTGTGGATGAAAAATGGTCTTTGTGCTCCCAGTCACCACTGGGGTCTGTTCTCTCTCTCTCTGCTGTTACAGTGTGGCTTTGGTTCTTGTTTCTTTGTTCTTTGGTCTGTAAATTACCCTTGAAACAACCCTTGAAATTTCCACTCCATGACCTAAATCGTCATCCCTAAATTGGTTACATACATATTTGGTGACACTTTGGAGGGGAAAAGCTTTATGTCTCTCTAACGTGTAGTTCTTAAGGGAATTTGCATATGGAAAAAACAGAGACTGCGTCTCTTAATTCC TCC SEQ ID NO: 7GGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGAGCAGGCAGCAGAGTGTCATAAAGAATTAACAACGTGGAACTCAGTTACTGGGATTTCTTCCATTCTCCTTTGATTCTCTAGACTAGAATTCCAAAGACCCTCAGGCTGGTGATGCAAGTGGGAAGTCTCATTTCTGAGAAGTGCTGCTTCCTACCCACAATTCTTTGATAGCTGAGTGCTTTAGCTGATCTGCATAACTGAGGTGTGCACCAAGGAGCAGAATTACTCTATAAATTTTGGCATCAACATGTGCAACTTGTGACTCAGCACTTTGAAACTCTGGGGATTTTTTTGTTTGGTTGGTTTTTGTTTTAAGATGTCCTGTGGTATAGTGGAAATAGTACAATAGACTCAGATACAGAGAGGCCTTGTTTCTAGTCTTGGTTCTGTCACTTACTATCTTGATGTCCTTGCACAAATCACCAGACCTCTCTGAGCCTCAGTTTCTCCAACCACACTGTGGGAATAATAAAATCTTTTTTACGGCATTGTTGTAAGTATGCAGAGAAACTGGTACACAGTAGCCACACAATCAATGTCACCGTACCCTTCAGCCCTTCTTTTGTGGATGAAAAATGGTCTTTGTGCTCCCAGTCACCACTGGGGTCTGTTCTCTCTCTCTCTGCTGTTACAGTGTGGCTTTGGTTCTTGTTTCTTTGTTCTTTGGTCTGTAAATTACCCTTGAAACAACCCTTGAAATTTCCACTCCATGACCTAAATCGTCATCCCTAAATTGGTTACATACATATTTGGTGACACTTTGGAGGGGAAAAGCTTTATGTCTCTCTAACGTGTAGTTCTTAAGGGAATTTGCATATGGAAAAAACAGAGACTGCGTCTCTTAATTCCTCC SEQ ID NO: 39TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTCTTCTTCAAAAGAGCCGCTGAAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGG GATGACTCTGGGA

ACAACTTACCTGAGCAAGCTGCTTTTTGGAGACATTTGCACATCTTTTGGGATCACGTTGTTAAGAAGTAGAACTAAGGGAAAAACACGCAGCCACCCAGAAATCGGTAGAGCCTTCAGCTCATCTGTTATTAATATTTCTGTGACAACAGATATCTAGGAAGTAAACAGGAAATTGCATCGCTATCCTGCATCACCTTTTTTGGAATCAGGTTCCATTCTTCTCAGTCCAGTTCAACCTTGTGATACTTTTTAGATCTCAACCAAGGCATAGAAATATATTTTCCCTTGCTTAATACCCCATGGAACCAATGCCCCTGTGGTTGAAGTAAAAATTGATTGTTGAGGGACATTTCAGCCCTCTAGCAGTCAACAATTAAAAACATGTAAGCACCGAGCACCTGCAGAAAACTTGGACTGGCATTTGGATCTAAGAAGAAAATCTGCATCTTGACCAAGATGAAAAGTCACCAGCCCAAGCTTGTGCAGTGAAGTGTCATGTTGGCCACAATGAAACTGAAAGAGACTGATGACTCTCCTCAGGGTGGAAAATGAGGCATGGAAGCTTTGATTAGTGAGCTGTTAGGCACACAGACATTAATTTCAAAGCATTCTCATCTCCAGTCTGAGTAATAATGCTTATAGTATTATGCAATTGTTTGGCTGCTGCAAGAAATTCAGCAGACTCCAACAAGTAGTCTTTCTTGGTCTCTGAGTGACTGTAACTTAAATTCTACCTCCCTTCTCTTCTCCTACATCTTCTCACTCCCCACCCCACCCCCACATACACACAATTCTTGTCCACTATGTTCAGAGAGATGCACGCACACATATATATGTATATATATAGTATATTTGTCAATAAAGCAGAAAAGAAGAAAAAACTCCAAGTAAACAATTTTCCATTTCCCCATCTCACTTCTGTCTTACAAGTGGATAGGAAAAGAAAAACCCCCAGTAAAAAATGGCAACCGCCCACCTCCCCAACTTTACATGCTGCTTCCTATGTTAGAGGATCTGTCTTAGGCATCTGATTATGGAGCCTGCTAGATACAAGCCCGTATTTAGACTGCTACAGTCAACAATGTCTCTCTTTCATACTAGAAAAATTCC SEQ ID NO: 8 C H Y G A L T C G S C K V F F KR A A E G K Q K Y L C A S R N D C T I D K F R RK N C P S C R L R K C Y E A G M T L G E K F R V G N C K H L K M T R PStop SEQ ID NO: 9 C H Y G A L T C G S C K V F F K R A A EG K Q K Y L C A S R N D C T I D K F R RK N C P S C R L R K C Y E A G M T L G  A V V V S E R I L R V F G V S E WL P Stop SEQ ID NO: 10 C H Y G A L T C G S C K V F F K R A A EG K Q K Y L C A S R N D C T I D K F R R K N C P S C R L RV K CY E A G M T L G G K Q K Y L C A S R N D C T I D K F R R K N C P S C R L R K C Y E A G M T L G  A V V V S E R I L R V F G V S E W L PStop SEQ ID NO: 11 C H Y G A L T C G S C K V F F K R A A E G F F R M N KL K E S S D T N P K P Y C M A A P M G L T E N N R N R K K S Y R E T N LK A V S W P L N H T Stop SEQ ID NO: 12 C H Y G A L T C G S C K V F F K RA A E G K Q K Y L C A S R N D C T I D K F R RK N C P S C R L R K C Y E A G M T L G G F F R M N K L K E S S D T N P KP Y C M A A P M G L T E N N R N R K K S Y R E T N L K A V S W P L N H TStop SEQ ID NO: 13G K Q K Y L C A S R N D C T I D K F R R K N C P S C R L 10R K C Y E A G M T L G D Stop SEQ ID NO: 14G K Q K Y L C A S R N D C T I D K F R R K N C P S C R L R K C Y E A G M T LG A G S R V S Stop SEQ ID NO: 40 C H Y G A L T C G S C K V F F K R A A EG K Q K Y L C A S R N D C T I D K F R RK N C P S C R L R K C Y E A G M T L G  D N L P E Q A A F W R H L H I F WD H V V K K Stop

Other aspects of the invention are described in or are obvious from thefollowing disclosure, and are within the ambit of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

The following Detailed Description, given by way of example, but notintended to limit the invention to specific embodiments described, maybe understood in conjunction with the accompanying drawings,incorporated herein by reference. Various preferred features andembodiments of the present invention will now be described by way ofnon-limiting example and with reference to the accompanying drawings inwhich:

FIG. 1A-C shows the cloning of novel AR variants. A, novel AR variantslacking LBD generated by splicing of four cryptic exons. The eightcanonical exons of the AR gene were represented by numbered open boxesand shown (not to scale) in relation to the genomic positions of thefour cryptic exons (CE1 to CE4) in shaded boxes. The identical forwardprimer, P1/P2/P3(F), in exon 2 was paired with three reverse primers (P1R, P2R, and P3R; see Table 2) designed based on Genbank entries for thethree transcribed genomic fragments in intron 3 (see Table 1).Sequencing of the amplicons (from CWR22Rv1 cells) defined the 5′junctions of CE1, CE2, and CE3, and 5′ and 3′ junctions of CE4, asmarked by vertical lines with the corresponding genomic coordinates(Human Genome Assembly March 2006, HG1 8). Note that there were fourCE1-containing variants (AR-V1, AR-V2, AR-V3, and AR-V4) and that thetwo CE2-containing variants (AR-V5 and AR-V6) differed by an 80-bpcontiguous 5′ extension in CE2. Stop codons were marked with thearrowheads in the schematically illustrated transcripts. The seventranslated protein sequences corresponding to the seven transcripts wereshown, starting from the last four amino acids encoded by exon 3 (AR-V1,AR-V2, AR-V4, AR-V5, AR-V6, and AR-V7) or exon 2 (AR-V3), and followedby variable lengths of variant-specific sequences in light gray thatmatched the cryptic exons. B, detection of the AR variant transcripts bysemiquantitative RT-PCR in clinical prostate specimens using the samesets of P1, P2, and P3 primers. HRPC (autopsy), metastatic HRPC samplesfrom autopsies; HRPC (TURP), HRPC samples from TURP; PCa (RRP),hormone-naive PCa from RRP specimens. C, amplification of full-lengthcoding region for AR-V1 and AR-V7 using primer sets P4 and P5 (Table 2)from one HRPC autopsy sample, one TURP sample, and the CWR22Rv1 cellline. Identical forward primers, P4(F) and P5(F) located upstream of thetranslation start codon in exon 1, were paired with reverse primers,P4(R) and P5(R), located downstream of the stop codon in cryptic exon 1and cryptic exon 3.

FIG. 2A-C shows quantification of AR variant transcripts in clinicalspecimens. A, representative gel images of amplified AR varianttranscripts detected using primer sets designed for real-time RT-PCRassays. An identical forward primer, P6/P7/P8(F), in exon 3 was pairedwith different reverse primers, P6(R), P7(R), and P8(R) (Table 2), toamplify the AR-V1, AR-V7, and prototype AR transcripts, respectively.SF3A3 was used as a reference gene transcript (Materials and Methods).Normal (RRP), normal prostate tissues from RRP specimens; PCa (RRP),hormone-naive PCa from RRP specimens; HRPC (TURP), HRPC samples fromTURP; HRPC (autopsy), metastatic HRPC samples from autopsies (Table 3).B, quantitative results of AR-V7 in 124 clinical prostate specimens byreal-time PCR. Normalized expression values (in log 2 scale) for AR-V7derived from comparative threshold analysis were shown in four groups ofclinical specimens. Normal (n=17), normal prostate tissues from RRPspecimens; Hormone naive PCa (n=82), PCa samples from RRP specimens;HRPC (TURP) (n=4), HRPC samples from TURP; HRPC (autopsy) (n=21),metastatic HRPC samples from autopsies (Table 3). C, Kaplan-Meier plotcomparing progression-free survival in patients with less than medianAR-V7 expression (n=38) with those with greater than median AR-V7expression (n=28). The survival curves were compared using the log-ranktest. Follow-up years were marked on the X axis. Censored subjects weremarked with vertical ticks in blue. Note that the PSA recurrence statuswas annotated in years, not months.

FIG. 3A-D shows AR-V7 protein detection and analysis using avariant-specific antibody. A, detection of AR-V7 protein product in celllines expressing high levels of AR-V7 transcript (see FIG. 5). Followingimmunoblot analysis for AR-V7 (top), the same membrane was stripped andsubjected to immunoblot analysis with anti-AR(N20) antibody (middle) todetect the prototype AR. Bottom, loading of total protein was monitoredby Ponceau S staining of the polyvinylidene difluoride (PVDF) membrane.B, detection of AR-V7 protein following enrichment of all NTD-containingAR proteins by IP using the anti-AR(441) antibody. Note that followingenrichment, AR-V7 was detected in cell lines expressing highest levelsof AR-V7 mRNA, VCaP and CWR22Rv1 cells, but not in LNCaP cells, whichexpressed low levels of AR-V7 (see FIG. 5). Control, mouse IgG; anti-AR,anti-AR(441) monoclonal antibody. C, detection of AR-V7 protein in HRPC.Western blot analysis was performed to detect AR-V7 in whole tissuelysates and enriched AR protein extracts derived from four hormone-naivehuman PCa tissue (RRP5, RRP6, RRP7, and RRP8) and two hormone-refractoryhuman PCa tissues (TURP1 and TURP2). Middle, protein loading wasmonitored by Ponceau S staining of the PVDF membrane; bottom, IP withthe anti-AR(441) antibody was performed to enrich the AR proteins andimmunoblotted (IB) with anti-AR(N20) to detect the prototype AR, andAR-V7 by the anti-AR-V7 antibody. D, biochemical analysis of cellularlocalization of AR-V7 protein. VCaP and CWR22Rv1 cells were grown inphenol red-free RPMI 1 640 containing CSS with or without 1 0 nmol/L R1881. The cytosolic fraction (C) and nuclear fraction (N) of lysates withequivalent number of cells were isolated and subjected to immunoblotanalysis of AR-V7, prototype AR by anti-AR(N20) antibody, and h-actin.

FIG. 4A-C shows constitutive function of AR-V7. A, constitutive nuclearlocalization of transfected AR-V7 in the absence of androgen. PC-3 cellswere transfected with pEGFP-AR and pEGFP-AR-V7 to express the prototypeAR or AR-V7 and examined for the localization of GFP-tagged AR proteinsin the presence or absence of 5 nmol/L R1 881. B, AR-V7 constitutivelyactivates an AR luciferase reporter. PC-3 cells were transfected withvector control (EGFP), a LBD-truncated AR mutant (EGFP-Q640X), AR-V7(EGFP-AR-V7), and prototype AR (EGFP-AR) and subjected to luciferaseassays and Western blot analysis following culturing in the presence orabsence of R1 881. C, androgen-independent induction of AR-responsivegenes by AR-V7 in LNCaP cells. LNCaP cells were transfected withpcDNA-AR-V7 to express the untagged AR-V7 protein or the control pcDNAvector and cultured with or without 10 nmol/L R1 881 before beingharvested for Western blot analysis or RNA extraction for expressionmicroarray analysis. The genes shown were the top 20 ranked genes byfold induction following R1 881 treatment in pcDNA emptyvector-transfected LNCaP cells. Expression ratios of the test sampleversus the common reference (pcDNA empty vector-transfected LNCaPwithout R1 881) were represented by red (>1) and green colors (<1).

FIG. 5 shows real time RT-PCR analysis of AR variants V1, and V7 inhuman prostate cancer cell lines. Normalized expression values (in log 2scale) for AR-V 1 (blue) and AR-V7 (red) derived from comparativethreshold analysis were shown in 9 human prostate cancer cells lines.LNCaP95 is an androgen-independent cell line derived from long-termcontinuous culture of LNCaP cells in androgen-depleted conditions,provided by Dr. Alan K. Meeker (Johns Hopkins University, Baltimore,Md.). VCaP and E006AA prostate cancer cells were provided by Dr. John T.Isaacs (Johns Hopkins University, Baltimore, Md.). Other human prostatecancer cells lines were obtained from the American Type CultureCollection (Rockville, Md.).

FIG. 6A-B shows Quantitative real-time RT-PCR results of prototype AR(A) and AR-V 1 (B) in 124 clinical prostate specimens. Normalizedexpression values (in log 2 scale) from comparative threshold analysiswere centered with the median of measurable values in 82 RRP cases setat zero. Normal (n=17): normal prostate tissues from radical retropubicprostatectomy (RRP) specimens; Hormone Naïve PCa (n=82): PCa samplesfrom RRP specimens; HRPC (TURP) (n=4): HRPC samples from transurethralresection of prostate (TURP); HRPC (autopsy) (n=21): metastatic HRPCsamples from autopsies (see Table 3).

FIG. 7A-B shows detection of AR-V7 transcripts using cytoplasmic ornuclear RNA extracted from LNCaP cells (A) and CWR22Rv1 cells (B). TheAgilent Bioanalyzer electropherograms were shown to the left and theexpression fold differences relative to the average value of nuclear RNA(from threshold cycle analysis) were shown to the right. The threesamples for each cell line correspond to nuclear and cytoplasmic RNAisolated from equal number of cells, and nuclear RNA from 6 fold excessof cells (6×nuclear RNA) to equalize the input nuclear RNA quantity withcytoplasmic RNA, as RNA yield/cell is ˜6 fold higher in the cytoplasmthan in then nucleus. Note that nuclear RNA is enriched for precursorrRNA (band above 28S rRNA). Also note that mature rRNA, but not mRNA,should be expected to be present in the nucleolus.

FIG. 8A-B shows Kaplan-Meier plot comparing progression free survival in66 patients with lower than median and higher than median expression ofprototype AR (AR-pt) expression (A) or ratio of AR-V7/AR-pt (B). Themedian value was identified based on all RRP cases (n=82) withmeasurable data points to be consistent with all similar analysesincluding data presented in FIG. 6B. The survival curves were comparedusing the Log-rank test. And p values of the tests were provided.Follow-up years were marked on the X axis. Censored subjects were markedwith vertical ticks in blue. Note that the PSA recurrence status wasannotated in years, not months.

FIG. 9A-B shows protein (A) and mRNA (B) expression analysis in 9hormone naïve RRP cases and 14 LuCaP human prostate cancer xenografts.Detection of AR-V7 and prototype AR protein was carried out usingstandard western immunoblots (IB) following enrichment of AR proteins byimmunoprecipitation (IP) using the anti-AR(441) antibody, whiledetection of the control β-actin protein was carried out using regularprotein lysate matched in quantity to the input lysate for IP. Note thatdata from different protein blots were not cross-comparable asexperimental variables were different while the mRNA data should becomparable across the all samples as AR-V7 mRNA expression levels werenormalized (in log 2 scale) and centralized to the median of the 82 RRPcases as presented in FIG. 2B. Xenografts specimens ending with AI (n=3)were androgen-independent derivative of the original xenograft followingandrogen ablation in the host animal. All xenografts originated fromHRPC patients except LuCaP 58 and LuCaP 115, which were from hormonenaïve lymph node metastasis.

FIG. 10A-C shows reduction of the 80 KD protein band following knockdown of the AR-V7 transcript or depletion of the AR-V7 protein usinganti-AR-V7 antibody. A. Transcript specific knock down of prototype AR(target sequence: UCAAGGAACUCGAUCGUAU; SEQ ID NO: 34) and AR-V7 (targetsequence: GUAGUUGUGAGUAUCAUGA; SEQ ID NO: 1). B. Standard immunoblotanalysis with anti-AR(N20), anti-AR-V7 and anti-β-actin antibodiesfollowing gene knock down. C. Standard immunoblot (IB) analysis withanti-AR(N20), anti-AR-V7 in CWR22Rv1 whole cell lysate followingdepletion of AR-V7 using anti-AR-V7 antibody. CWR22Rv1 cell lysate wasincubated with protein G resin coupled to anti-AR-V7 antibody to depleteAR-V7 (anti-AR-V7 depleted) or protein G resin alone as a control (nodepletion).

FIG. 11 shows the ratio of AR-V7 versus prototype AR (AR-pt) in 24 HRPCspecimens (red) and 81 hormone naïve RRP cases (Blue). The cases wereidentical to those presented in FIG. 2B, expect that 2 cases wereexcluded due to uncalculable ratios. Despite a trend of higher AR-V7versus prototype AR (AR-Pt) in a subset of HRPC specimens, the overalldifference between RRP (median ratio 1:389) and HRPC (median ratio1:238) specimens is not significant (p=0.0841, Mann-Whitney test). Theabsolute ratio values were calculated based on real-time RT-PCRexpression values extrapolated upon standard curves of serial dilutionsspanning 9 orders of magnitudes of known quantities of the targetamplicons (plasmids harboring either AR-V7 or prototype AR).

FIG. 12A-C shows development of polyclonal mouse anti-human AR-V7antibody. The panels show testing initial bleeds from 6 mice immunizedwith peptide sequences specific to AR-V7 (CKHLKMRP; SEQ ID NO: 1). A.ELISA results (plate (A) and log sheet (B)) using two differentpreparations of coating peptide antigens. JHU014 (top half of the plate)antigen was the same as the immunogen, while JHU016 antigen (bottom halfof the plate) has identical sequence but made separately. C. westernblot to test the antibody. CWR22Rv1 whole cell lysates were used. Serumwas diluted 1:1000. The molecular weight of the AR-V7 antigen isexpected to be ˜75-80 KD. The position of the 75 Kda protein marker wasindicated by an arrow. Relatively specific positive signals weredetected in mouse #2, 4, and 5.

FIG. 13 shows western blot analysis of subsequent bleeds (followingboosting) from mouse #1 and #2 (Ab used at 1:1000 dilution). Specificdetection of AR-V7 antigen was performed using 293 T cells transfectedwith control vector (293T no transfection) or vector whichover-expresses AR-V7 (293T+AR-V7), as well as PC-3 (negative control)and CWR22Rv1 whole cell lysates (WCL) (positive control). Based on theresult, JHU019#2 mouse was chosen for fusion and subsequent hybridomageneration.

FIG. 14A-B shows initial hybridma screening results shown in scannedimage (A) of the ELISA plates and a log sheet (B). Strong positivesignals were detected in well 4E4 and 2D12. The positive control ispolyclonal serum at 1:1000 dilution, on plate 4 in well H5 (4H5).

FIG. 15A-B shows confirmatory ELISA results of selected clones inscanned log sheet (B) and plate image (A). Clone IDs corresponding tothe original plate and well designations were shown in the log sheet toindicate their position in this assayed plate. The top half of the platewas used to detect IgG while the bottom half designed to detect IgM.2D12 was confirmed as a strong IgG positive clone. Other candidateclones were also expanded for downstream analysis. These included 2B6(IgM), 4F7 (IgM), 4E4 (IgM), and 1A1 (IgG). PC: positive control whichwas serum at 1:1000 dilution.

FIG. 16 shows selection of the positive monoclonal anti-AR-V7hybridomas. Further confirmation of the 5 selected clones from FIG. 4.Whole cell lysates harvested from 293T cell transfected with AR-V7over-expression plasmids were resolved on SDS-PAGE gel and transferredto PDVF membrane. Membrane slices (1 cm×1 cm) corresponding to thelocation of the 75 Kda bands were subjected to immuno blot with eachindividual hybridoma supernatant diluted 1:2. Ployclonal serum (JHU019)from mouse #2 was used as positive control. Based on this result, clone2D12 was selected for expansion while the rest were discarded.

FIG. 17 shows confirmation of antibody specificity for clone 2D12.CWR22Rv1 cells were transfected with control siRNA or AR-V7 siRNA yoknockdwon endogenous AR-V7 expression. 96 hours later, whole celllysates were harvested and subjected to immunoblot with 2D12supernatantat 1:2 dilution.

FIG. 18A-D shows in vivo staining of AR-V7 in CWR22Rv1 cells (A and B)and clinical prostate cancer specimens (C, D). Panel B showsimmunofluorescent detection of AR-V7 predominantly in the nuclei ofCWR22Rv1 cells (B). Panel A is DAPI staining to show the nuclei in thesame cells. Panel C is a H&E stained section of hormone naïve prostatecancer specimen from a patient who later received and failed hormonetherapy. This specimen is positive for AR-V7 protein expression asdetected by immunoblots (supplemental data FIG. 5A of Hu et al. CancerResearch 69 (1):16-22, 2009). Shown in Panel D is the predominantlynuclear staining of AR-V7 and negative staining in the adjacent normalstromal tissues. Panel C and D are adjacent cuts of the same tissueblock.

FIG. 19A-B shows AR-V7 promotes androgen independent growth of LNCaPcells. LNCaP cells were transfected by AR-V7 and the control vector. A.Cell growth in medium supplemented with charcoal stripped serum (CSS) inabsence or presence of 0.5 nM R1881 were monitored by MTS assay. Ectopicexpression of AR-V7 in LNCaP cells was confirmed by western blotanalysis (B). As shown the growth rates of AR-V7 expressing cellssurpassed those of parental cells cultured in the presence of syntheticandrogen R1881.

FIG. 20 shows tiling array results viewed by the Affyrnetrix IntegratedGenome Browser. The canonical exons and intron boundaries are shown inrelation to the genomic coordinates (HG18, March 2006 release) in thetop strip and data from the CWR22Rv1 (yellow) cells and a hormonerefractory prostate cancer specimen (TURP2) (blue) shown with the signalintensities (y axis) across the genomic coordinates (x axis) of thehuman AR gene. Note intense signal for AR-V7 variant specific sequences(the start position of the AR-V7 variant specific sequence is marked byan arrow), and the intense signal from AR-V8 specific sequences (thestart position of the AR-V8 variant specific sequence is marked by anarrow) immediately upstream of AR-V7. The primer used to amplify AR-V8is as follows: 5′-Tgtcactatggagctctcacatgtgg-3′ and5′-Cattgtggccaacatgacacttca-3′.

DETAILED DESCRIPTION OF THE INVENTION I. Definitions

Unless defined otherwise, all technical and scientific terms used hereinhave the meaning commonly understood by a person skilled in the art towhich this invention belongs. The following references provide one ofskill with a general definition of many of the terms used in thisinvention: Singleton et al., Dictionary of Microbiology and MolecularBiology (2nd ed. 1994); The Cambridge Dictionary of Science andTechnology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R.Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, TheHarper Collins Dictionary of Biology (1991). As used herein, thefollowing terms have the meanings ascribed to them unless specifiedotherwise.

By “antibody” is meant any immunoglobulin polypeptide, or fragmentthereof, having immunogen binding ability.

By “androgen receptor” (AR) is meant a member of the steroid hormonereceptor family of molecules. AR mediates the physiologic effects ofandrogens by binding to DNA sequences that influence transcription orandrogen-responsive genes. The wild-type AR mRNA reference sequencecorresponds to GenBank database Accession No. NM 000044 (correspondingto SEQ ID NO: 34).

By “androgen receptor polypeptide” is meant a protein or proteinvariant, or fragment thereof, that is substantially identical to atleast a portion of GenBank Accession No. NP 000035 (Corresponding to SEQID NO: 35) and that has an androgen receptor biological activity.

By “androgen receptor nucleic acid molecule” is meant a polynucleotideencoding an androgen receptor polypeptide or variant, or fragmentthereof.

By “androgen related disease or disorder” is meant to refer to anydisease or disorder that results from an imbalance of androgen in thebody. Examples of androgen related diseases or disorders includeprostate cancer, androgenic alopecia, infertility, irregular menstrualperiods, excessive hair growth, acne, obesity and insulin resistance,and polycystic ovarian syndrome.

The term “amino acid” refers to naturally occurring and synthetic aminoacids, as well as amino acid analogs and amino acid mimetics thatfunction in a manner similar to the naturally occurring amino acids.Naturally occurring amino acids are those encoded by the genetic code,as well as those amino acids that are later modified, for example,hydroxyproline, gamma-carboxyglutamate, and O-phosphoserine,phosphothreonine.

By “biomarker” is meant any protein or polynucleotide having analteration in expression level or activity that is associated with adisease or disorder, for example an androgen related disease ordisorder.

By “detectable amino acid sequence” or “detectable moiety” is meant acomposition that when linked with the nucleic acid or protein moleculeof interest renders the latter detectable, via any means, includingspectroscopic, photochemical, biochemical, immunochemical, or chemicalmeans. For example, useful labels include radioactive isotopes, magneticbeads, metallic beads, colloidal particles, fluorescent dyes,electron-dense reagents, enzymes (for example, as commonly used in anELISA), biotin, digoxigenin, or haptens.

A “labeled nucleic acid or oligonucleotide probe” is one that is bound,either covalently, through a linker or a chemical bond, ornoncovalently, through ionic bonds, van der Waals forces, electrostaticattractions, hydrophobic interactions, or hydrogen bonds, to a labelsuch that the presence of the nucleic acid or probe may be detected bydetecting the presence of the label bound to the nucleic acid or probe.

An “expression vector” is a nucleic acid construct, generatedrecombinantly or synthetically, bearing a series of specified nucleicacid elements that enable transcription of a particular gene in a hostcell. Typically, gene expression is placed under the control of certainregulatory elements, including constitutive or inducible promoters,tissue-preferred regulatory elements, and enhancers.

By “fragment” is meant a portion (e.g., at least 10, 25, 50, 100, 125,150, 200, 250, 300, 350, 400, or 500 amino acids or nucleic acids) of aprotein or nucleic acid molecule that is substantially identical to areference protein or nucleic acid and retains the biological activity ofthe reference. In some embodiments the portion retains at least 50%,75%, or 80%, or more preferably 90%, 95%, or even 99% of the biologicalactivity of the reference protein or nucleic acid described herein.

A “host cell” is any prokaryotic or eukaryotic cell that contains eithera cloning vector or an expression vector. This term also includes thoseprokaryotic or eukaryotic cells that have been genetically engineered tocontain the cloned gene(s) in the chromosome or genome of the host cell.

By “inhibitory nucleic acid” is meant a double-stranded RNA, siRNA(short interfering RNA), shRNA (short hairpin RNA), or antisense RNA, ora portion thereof, or a mimetic thereof, that when administered to amammalian cell results in a decrease (e.g., by 10%, 25%, 50%, 75%, oreven 90-100%) in the expression of a target gene. Typically, a nucleicacid inhibitor comprises at least a portion of a target nucleic acidmolecule, or an ortholog thereof, or comprises at least a portion of thecomplementary strand of a target nucleic acid molecule.

The terms “isolated,” “purified,” or “biologically pure” refer tomaterial that is free to varying degrees from components which normallyaccompany it as found in its native state. Various levels of purity maybe applied as needed according to this invention in the differentmethodologies set forth herein; the customary purity standards known inthe art may be used if no standard is otherwise specified.

By “isolated nucleic acid molecule” is meant a nucleic acid (e.g., aDNA, RNA, or analog thereof) that is free of the genes which, in thenaturally-occurring genome of the organism from which the nucleic acidmolecule of the invention is derived, flank the gene. The term thereforeincludes, for example, a recombinant DNA that is incorporated into avector; into an autonomously replicating plasmid or virus; or into thegenomic DNA of a prokaryote or eukaryote; or that exists as a separatemolecule (for example, a cDNA or a genomic or cDNA fragment produced byPCR or restriction endonuclease digestion) independent of othersequences. In addition, the term includes an RNA molecule which istranscribed from a DNA molecule, as well as a recombinant DNA which ispart of a hybrid gene encoding additional polypeptide sequence.

“Microarray” is meant to refer to a collection of nucleic acid moleculesor polypeptides from one or more organisms arranged on a solid support(for example, a chip, plate, or bead).

By “nucleic acid” is meant an oligomer or polymer of ribonucleic acid ordeoxyribonucleic acid, or analog thereof. This term includes oligomersconsisting of naturally occurring bases, sugars, and intersugar(backbone) linkages as well as oligomers having non-naturally occurringportions which function similarly. Such modified or substitutedoligonucleotides are often preferred over native forms because ofproperties such as, for example, enhanced stability in the presence ofnucleases.

“Complimentary nucleic acid sequences” refer to contiguous DNA or RNAsequences which have compatible nucleotides (e.g., A/T, G/C) incorresponding positions, such that base pairing between the sequencesoccurs. For example, the sense and anti-sense strands of adouble-stranded DNA helix are known in the art to be complimentary.

By “protein” is meant any chain of amino acids, or analogs thereof,regardless of length or post-translational modification.

By “reference” is meant a standard or control condition.

By “siRNA” is meant a double stranded RNA. Optimally, an siRNA is 18,19, 20, 21, 22, 23 or 24 nucleotides in length and has a 2 base overhangat its 3′ end. These dsRNAs can be introduced to an individual cell orto a whole animal; for example, they may be introduced systemically viathe bloodstream. Such siRNAs are used to downregulate mRNA levels orpromoter activity.

By “specifically binds” is meant a molecule (e.g., peptide,polynucleotide) that recognizes and binds a protein or nucleic acidmolecule of the invention, but which does not substantially recognizeand bind other molecules in a sample, for example, a biological sample,which naturally includes a protein of the invention.

By “substantially identical” is meant a protein or nucleic acid moleculeexhibiting at least 50% identity to a reference amino acid sequence (forexample, any one of the amino acid sequences described herein) ornucleic acid sequence (for example, any one of the nucleic acidsequences described herein). Preferably, such a sequence is at least60%, more preferably 80% or 85%, and most preferably 90%, 95% or even99% identical at the amino acid level or nucleic acid to the sequenceused for comparison.

Sequence identity is typically measured using sequence analysis software(for example, Sequence Analysis Software Package of the GeneticsComputer Group, University of Wisconsin Biotechnology Center, 1710University Avenue, Madison, Wis. 53705, BLAST, BESTFIT, GAP, orPILEUP/PRETTYBOX programs). Such software matches identical or similarsequences by assigning degrees of homology to various substitutions,deletions, and/or other modifications. Conservative substitutionstypically include substitutions within the following groups: glycine,alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid,asparagine, glutamine; serine, threonine; lysine, arginine; andphenylalanine, tyrosine. In an exemplary approach to determining thedegree of identity, a BLAST program may be used, with a probabilityscore between e-3 and e-100 indicating a closely related sequence.

Other definitions appear in context throughout the disclosure.

METHODS OF THE INVENTION

The invention features compositions and methods useful for the diagnosisand prognosis of androgen related diseases or disorders in a subject.The invention features compositions and methods useful for detecting,treating or preventing prostate cancer. These methods and compositionsare based, in part, on the discovery that expression of certain androgenreceptor variants is elevated in certain prostate cancers. The inventionalso provides methods and compositions for altering androgen receptorvariant expression, and may be useful, for example, for the treatment ofandrogen related diseases, such as prostate cancer.

In particular, the invention is based on the finding that particularandrogen receptor variants lacking the ligand binding domain (LBD), butthat retained intact coding potential for the full androgen receptorNH2-terminal domain (NTD) and DNA-binding domain (DBD), wereoverexpressed in hormone refractory prostate cancer. One of thevariants, AR-V7, was expressed at elevated levels in a subset of hormonenaïve prostate cancers that recurred after surgical treatment.

Androgen Receptor Variants

The androgen receptor (AR) is a member of the steroid hormone receptorfamily of molecules. The AR primarily is responsible for mediating thephysiologic effects of androgens by binding to specific DNA sequencesthat influence transcription or androgen-responsive genes. The human ARgene is located on chromosome Xq11-12 and spans approximately 180 kb ofDNA containing eight exons that code for an approximately 2,757 basepair open reading frame within a 10.6 kb mRNA (Gelmann 2002). This genestructure is evolutionarily conserved among the sex steroid hormonereceptors. The AR protein product is approximately 919 amino acids longand has a number of functional domains. The first exon codes for theN-terminal domain (NTD), which is the transcriptional regulatory regionof the protein, exons 2 and 3 code for the central DNA binding domain(DBD), the first part of exon 4 encodes a hinge region, and exons 4-8code for the C-terminal ligand-binding domain (LBD). A schematic diagramof the AR gene and protein can be seen in FIG. 1A. Genomic sequence forthe human AR gene was obtained from the 2006 NCBI human genome assembly(HG 18). The sequence spans nucleotides 66680599-66860844 on chromosomeX. The wild-type AR mRNA reference sequence corresponds to GenBankdatabase Accession No. NM_000044.2, shown below, and corresponding toSEQ ID NO: 34.

SEQ ID NO: 34 1 cgagatcccg gggagccagc ttgctgggag agcgggacgg tccggagcaagcccagaggc 61 agaggaggcg acagagggaa aaagggccga gctagccgct ccagtgctgtacaggagccg 121 aagggacgca ccacgccagc cccagcccgg ctccagcgac agccaacgcctcttgcagcg 181 cggcggcttc gaagccgccg cccggagctg ccctttcctc ttcggtgaagtttttaaaag 241 ctgctaaaga ctcggaggaa gcaaggaaag tgcctggtag gactgacggctgcctttgtc 301 ctcctcctct ccaccccgcc tccccccacc ctgccttccc cccctcccccgtcttctctc 361 ccgcagctgc ctcagtcggc tactctcagc caacccccct caccacccttctccccaccc 421 gcccccccgc ccccgtcggc ccagcgctgc cagcccgagt ttgcagagaggtaactccct 481 ttggctgcga gcgggcgagc tagctgcaca ttgcaaagaa ggctcttaggagccaggcga 541 ctggggagcg gcttcagcac tgcagccacg acccgcctgg ttaggctgcacgcggagaga 601 accctctgtt ttcccccact ctctctccac ctcctcctgc cttccccaccccgagtgcgg 661 agccagagat caaaagatga aaaggcagtc aggtcttcag tagccaaaaaacaaaacaaa 721 caaaaacaaa aaagccgaaa taaaagaaaa agataataac tcagttcttatttgcaccta 781 cttcagtgga cactgaattt ggaaggtgga ggattttgtt tttttcttttaagatctggg 841 catcttttga atctaccctt caagtattaa gagacagact gtgagcctagcagggcagat 901 cttgtccacc gtgtgtcttc ttctgcacga gactttgagg ctgtcagagcgctttttgcg 961 tggttgctcc cgcaagtttc cttctctgga gcttcccgca ggtgggcagctagctgcagc 1021 gactaccgca tcatcacagc ctgttgaact cttctgagca agagaaggggaggcggggta 1081 agggaagtag gtggaagatt cagccaagct caaggatgga agtgcagttagggctgggaa 1141 gggtctaccc tcggccgccg tccaagacct accgaggagc tttccagaatctgttccaga 1201 gcgtgcgcga agtgatccag aacccgggcc ccaggcaccc agaggccgcgagcgcagcac 1261 ctcccggcgc cagtttgctg ctgctgcagc agcagcagca gcagcagcagcagcagcagc 1321 agcagcagca gcagcagcag cagcagcagc agcaagagac tagccccaggcagcagcagc 1381 agcagcaggg tgaggatggt tctccccaag cccatcgtag aggccccacaggctacctgg 1441 tcctggatga ggaacagcaa ccttcacagc cgcagtcggc cctggagtgccaccccgaga 1501 gaggttgcgt cccagagcct ggagccgccg tggccgccag caaggggctgccgcagcagc 1561 tgccagcacc tccggacgag gatgactcag ctgccccatc cacgttgtccctgctgggcc 1621 ccactttccc cggcttaagc agctgctccg ctgaccttaa agacatcctgagcgaggcca 1681 gcaccatgca actccttcag caacagcagc aggaagcagt atccgaaggcagcagcagcg 1741 ggagagcgag ggaggcctcg ggggctccca cttcctccaa ggacaattacttagggggca 1801 cttcgaccat ttctgacaac gccaaggagt tgtgtaaggc agtgtcggtgtccatgggcc 1861 tgggtgtgga ggcgttggag catctgagtc caggggaaca gcttcggggggattgcatgt 1921 acgccccact tttgggagtt ccacccgctg tgcgtcccac tccttgtgccccattggccg 1981 aatgcaaagg ttctctgcta gacgacagcg caggcaagag cactgaagatactgctgagt 2041 attccccttt caagggaggt tacaccaaag ggctagaagg cgagagcctaggctgctag 2101 gcagcgctgc agcagggagc tccgggacac ttgaactgcc gtctaccctgtctctctaca 2161 agtccggagc actggacgag gcagctgcgt accagagtcg cgactactacaactttccac 2221 tggctctggc cggaccgccg ccccctccgc cgcctcccca tccccacgctcgcatcaagc 2281 tggagaaccc gctggactac ggcagcgcct gggcggctgc ggcggcgcagtgccgctatg 2341 gggacctggc gagcctgcat ggcgcgggtg cagcgggacc cggttctgggtcaccctcag 2401 ccgccgcttc ctcatcctgg cacactctct tcacagccga agaaggccagttgtatggac 2461 cgtgtggtgg tggtgggggt ggtggcggcg gcggcggcgg cggcggcggcggcggcggcg 2521 gcggcggcgg cggcgaggcg ggagctgtag ccccctacgg ctacactcggccccctcagg 2581 ggctggcggg ccaggaaagc gacttcaccg cacctgatgt gtggtaccctggcggcatgg 2641 tgagcagagt gccctatccc agtcccactt gtgtcaaaag cgaaatgggcccctggatgg 2701 atagctactc cggaccttac ggggacatgc gtttggagac tgccagggaccatgttttgc 2761 ccattgacta ttactttcca ccccagaaga cctgcctgat ctgtggagatgaagcttctg 2821 ggtgtcacta tggagctctc acatgtggaa gctgcaaggt cttcttcaaaagagccgctg 2881 aagggaaaca gaagtacctg tgcgccagca gaaatgattg cactattgataaattccgaa 2941 ggaaaaattg tccatcttgt cgtcttcgga aatgttatga agcagggatgactctgggag 3001 cccggaagct gaagaaactt ggtaatctga aactacagga ggaaggagaggcttccagca 3061 ccaccagccc cactgaggag acaacccaga agctgacagt gtcacacattgaaggctatg 3121 aatgtcagcc catctttctg aatgtcctgg aagccattga gccaggtgtagtgtgtgctg 3181 gacacgacaa caaccagccc gactcctttg cagccttgct ctctagcctcaatgaactgg 3241 gagagagaca gcttgtacac gtggtcaagt gggccaaggc cttgcctggcttccgcaact 3301 tacacgtgga cgaccagatg gctgtcattc agtactcctg gatggggctcatggtgtttg 3361 ccatgggctg gcgatccttc accaatgtca actccaggat gctctacttcgcccctgatc 3421 tggttttcaa tgagtaccgc atgcacaagt cccggatgta cagccagtgtgtccgaatga 3481 ggcacctctc tcaagagttt ggatggctcc aaatcacccc ccaggaattcctgtgcatga 3541 aagcactgct actcttcagc attattccag tggatgggct gaaaaatcaaaaattctttg 3601 atgaacttcg aatgaactac atcaaggaac tcgatcgtat cattgcatgcaaaagaaaaa 3661 atcccacatc ctgctcaaga cgcttctacc agctcaccaa gctcctggactccgtgcagc 3721 ctattgcgag agagctgcat cagttcactt ttgacctgct aatcaagtcacacatggtga 3781 gcgtggactt tccggaaatg atggcagaga tcatctctgt gcaagtgcccaagatccttt 3841 ctgggaaagt caagcccatc tatttccaca cccagtgaag cattggaaaccctatttccc 3901 caccccagct catgccccct ttcagatgtc ttctgcctgt tataactctgcactactcct 3961 ctgcagtgcc ttggggaatt tcctctattg atgtacagtc tgtcatgaacatgttcctga 4021 attctatttg ctgggctttt tttttctctt tctctccttt ctttttcttcttccctccct 4081 atctaaccct cccatggcac cttcagactt tgcttcccat tgtggctcctatctgtgttt 4141 tgaatggtgt tgtatgcctt taaatctgtg atgatcctca tatggcccagtgtcaagttg 4201 tgcttgttta cagcactact ctgtgccagc cacacaaacg tttacttatcttatgccacg 4261 ggaagtttag agagctaaga ttatctgggg aaatcaaaac aaaaacaagcaaac

The wild-type AR protein reference sequence corresponds to GenBankdatabase Accession No. NP 000035, shown below, and corresponding to SEQID NO: 35.

SEQ ID NO: 35 1 mevqlglgrv yprppsktyr gafqnlfqsv reviqnpgpr hpeaasaappgasllllqqq 61 qqqqqqqqqq qqqqqqqqqq etsprqqqqq qgedgspqah rrgptgylvldeeqqpsqpq 121 salechperg cvpepgaava askglpqqlp appdeddsaa pstlsllgptfpglsscsad 181 lkdilseast mqllqqqqqe aysegsssgr areasgapts skdnylggtstisdnakelc 241 kaysysmglg vealehlspg eqlrgdcmya pllgvppavr ptpcaplaeckgsllddsag 301 kstedtaeys pfkggytkgl egeslgcsgs aaagssgtle lpstlslyksgaldeaaayq 361 srdyynfpla lagppppppp phpharikle npldygsawa aaaaqcrygdlaslhgagaa 421 gpgsgspsaa assswhtlft aeegqlygpc gggggggggg gggggggggggggeagavap 481 ygytrppqgl agqesdftap dvwypggmvs rvpypsptcv ksemgpwmdsysgpygdmrl 541 etardhvlpi dyyfppqktc licgdeasgc hygaltcgsc kvffkraaegkqkylcasrn 601 dctidkfrrk ncpscrlrkc yeagmtlgar klkklgnlkl qeegeassttspteettqkl 661 tvshiegyec qpiflnvlea iepgvvcagh dnnqpdsfaa llsslnelgerqlvhvvkwa 721 kalpgfrnlh vddqmaviqy swmglmvfam gwrsftnvns rmlyfapdlvfneyrmhksr 781 mysqcvrrnrh lsqefgwlqi tpqeflcmka lllfsiipvd glknqkffdelrmnyikeld 841 riiackrknp tscsrrfyql tklldsvqpi arelhqftfd llikshmvsvdfpemmaeii 901 svqvpkilsg kvkpiyfhtq

The present invention describes novel androgen receptor variants thatlack the androgen receptor ligand binding domain (LBD). The presentinvention describes multiple novel androgen receptor LBD transcriptvariants with intact coding potential for the full androgen receptor NTDand androgen receptor DBD, but impaired coding potential for theandrogen receptor LBD. Each of the variants can be uniquely identifiedby its variant-specific sequence. It is a finding of the presentinvention that these novel AR transcripts were overexpressed in hormonerefractory prostate cancer (HPRC) and one of the most abundant variants,AR-V7, was expressed at elevated levels in a subset of hormone-naive PCathat recurred after surgical treatment.

Accordingly, the invention features polypeptides comprising an isolatedandrogen receptor protein variant, or fragment thereof, havingsubstantial identity to androgen receptor variant 1, 2, 3, 4, 5, 6, 7 or8 (AR-V1-AR-V8), wherein the variant is upregulated in an androgenrelated disease or disorder. In particular examples, the polypeptidecomprising an isolated androgen receptor protein variant, or fragmentthereof, having substantial identity to androgen receptor variant 1, 2,3, 4, 5, 6, 7 or 8 (AR-V1-AR-V8) is upregulated in prostate cancer.

Preferably, the androgen receptor protein variant is at least 85%identical to androgen receptor variant 1, 2, 3, 4, 5, 6, 7 or 8.

As described herein the androgen receptor protein variant comprises theandrogen receptor NH2 terminal domain (NTD), DNA binding domain (DBD),and the c-terminal variant specific peptide sequence that uniquelyidentifies each variant.

In certain preferred examples, the androgen receptor variant nucleicacid comprises a sequence selected from any one or more of SEQ ID NO: 1,SEQ ID NO: 39, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5,SEQ ID NO: 6 and SEQ ID NO: 7 or fragments thereof.

SEQ ID NO: 1 corresponds to the nucleotide sequence of transcript AR V7.Most of the upstream sequence common to all androgen receptors,corresponding to nucleotide 1-2822 of SEQ ID NO: 34, is not included.The first nucleotide of the variant specific sequences is shaded.

SEQ ID NO: 2 TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTCTTCTTCAAAAGAGCCGCTGAAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGA

AAAAATTCCGGGTTGGC AATTGCAAGCATCTCAAAATGACCAGACCCTGAAGAAAGGCTGACTTGCCTCATTCAAAATGAGGGCTCTAGAGGGCTCTAGTGGATAGTCTGGAGAAACCTGGCGTCTGAGGCTTAGGAGCTTAGGTTTTTGCTCCTCAACACAGACTTTGACGTTGGGGTTGGGGGCTACTCTCTTGATTGCTGACTCCCTCCAGCGGGACCAATAGTGTTTTCCTACCTCACAGGGATGTTGTGAGGACGGGCTGTAGAAGTAATAGTGGTTACCACTCATGTAGTTGTGAGTATCATGATTATTGTTTCCTGTAATGTGGCTTGGCATTGGCAAAGTGCTTTTTGATTGTTCTTGATCACATATGATGGGGGCCAGGCACTGACTCAGGCGGATGCAGTGAAGCTCTGGCTCAGTCGCTTGCTTTTCGTGGTGTGCTGCCAGGAAGAAACTTTGCTGATGGGACTCAAGGTGTCACCTTGGACAAGAAGCAACTGTGTCTGTCTGAGGTTCCTGTGGCCATCTTTATTTGTGTATTAGGCAATTCGTATTTCCCCCTTAGGTTCTAGCCTTCTGGATCCCAGCCAGTGACCTAGATCTTAGCCTCAGGCCCTGTCACTGAGCTGAAGGTAGTAGCTGATCCACAGAAGTTCAGTAAACAAGGACCAGATTTCTGCTTCTCCAGGAGAAGAAGCCAGCCAACCCCTCTCTTCAAACACACTGAGAGACTACAGTCCGACTTTCCCTCTTACATCTAGCCTTACTGTAGCCACACTCCTTGATTGCTCTCTCACATCACATGCTTCTCTTCATCAGTTGTAAGCCTCTCATTCTTCTCCCAAGCCAGACTCAAATATTGTATTGATGTCAAAGAAGAATCACTTAGAGTTTGGAATATCTTGTTCTCTCTCTGCTCCATAGCTTCCATATTGACACCAGTTTCTTTCTAGTGGAGAAGTGGAGTCTGTGAAGCCAGGGAAACACACATGTGAGAGTCAGAAGGACTCT CCC

SEQ ID NO: 2 corresponds to the nucleotide sequence of transcript AR V1.Most of the upstream sequence common to all androgen receptors,corresponding to nucleotide 1-2822 of SEQ ID NO: 34, is not included.The first nucleotide of the variant specific sequences is shaded.

SEQ ID NO: 3 TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTCTTCTTCAAAAGAGCCGCTGAAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGA

CTGTTGTTGTTTCTGAA AGAATCTTGAGGGTGTTTGGAGTCTCAGAATGGCTTCCTTAAAGACTACCTTCAGACTCTCAGCTGCTCATCCACAACAGAGATCAGCCTTTCTTTGTAGATGATTCATTCCTGGCTGCATTTGAAAACCACATATTGTTAATTGCTTGACGAATTTAAATCCCTTGACTACTTTTCATTTCAGAAAACACTTACAAAAAAAGTCCAAATGAGGACCTTCCCTCCAGTGAATTAGCTGTGGCTTTCTCACAGTCCATAGTTAGGATAAATGTAAAGCCATTTCTCATTTTTCTCCGCACTTTCCAAGGGTACACTCCTTGTTTCCAAGATGGAATGAGAAATAAAGAAGTGCCCTTCCTGCCATCTTCTCCCCTGACCCTTTCCTCCTTCCCACTTTCCTCCTATTCCTCCCCAAACATGATTTATTTCTGCGTTTTGCAACTCTTGAGTTCTCAGCATTTAGTAAATGGTGTTGGTCCCTGTTGATTCCTTCCTCTCCTGGACCATGGAAGGTAGTAGGCCTTTCAGAAATTTCAGGTAGCAGCCAAACCCCAGAAGAAGAGAAGGAACACAGAGACCTAGACCATGTGAGAACCTGAGGTGTGCAGCATTTACTTCACAGATTCGTCTAGCATATTTGAGAGGTG

SEQ ID NO: 3 corresponds to the nucleotide sequence of transcript AR V2.Most of the upstream sequence common to all androgen receptors,corresponding to nucleotide 1-2822 of SEQ ID NO: 34, is not included.The first nucleotide of the variant specific sequences is shaded.

SEQ ID NO: 4 TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTCTTCTTCAAAAGAGCCGCTGAAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGA

CTGTTGTTGTTTCTGAAAGAATCTTGAGGGTGTTTGGAGTCTCAGAATGGCTTCCTTAAAGACTACCTTCAGACTCTCAGCTGCTCATCCACAACAGAGATCAGCCTTTCTTTGTAGATGATTCATTCCTGGCTGCATTTGAAAACCACATATTGTTAATTGCTTGACGAATTTAAATCCCTTGACTACTTTTCATTTCAGAAAACACTTACAAAAAAAGTCCAAATGAGGACCTTCCCTCCAGTGAATTAGCTGTGGCTTTCTCACAGTCCATAGTTAGGATAAATGTAAAGCCATTTCTCATTTTTCTCCGCACTTTCCAAGGGTACACTCCTTGTTTCCAAGATGGAATGAGAAATAAAGAAGTGCCCTTCCTGCCATCTTCTCCCCTGACCCTTTCCTCCTTCCCACTTTCCTCCTATTCCTCCCCAAACATGATTTATTTCTGCGTTTTGCAACTCTTGAGTTCTCAGCATTTAGTAAATGGTGTTGGTCCCTGT TGAT

CCTTCCTCTCCTGGACCATGGAAGGTAGTAGGCCTTTCAGAAATTTCAGGTAGCAGCCAAACCCCAGAAGAAGAGAAGGAACACAGAGACCTAGACCATGTGAGAACCTGAGGTGTGCAGCATTTACTTCACAGATTCGT CTAGCATATTTGAGAGGTG

SEQ ID NO: 4 corresponds to the nucleotide sequence of transcript AR V3.Most of the upstream sequence common to all androgen receptors,corresponding to nucleotide 1-2822 of SEQ ID NO: 34, is not included.The first nucleotide of the variant specific sequences is shaded.

SEQ ID NO: 5 TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTCTTCTTCAAAAGAGCCGCTGAA

GATTTTTCAGAATGAACAAATTAAAAGAATCATCAGACACTAACCCCAAGCCATACTGCATGGCAGCACCAATGGGACTGACAGAAAACAACAGAAATAGGAAGAAATCCTACAGAGAAACAAACTTGAAAGCTGTCTCATGGCCTTTGAATCATACTTAAGTTTTATGATGGAAGGATACGACTATGAAGAAAGACACAGAGCAACATCAGACAGTCAAGAATTTCAGAGCCAGCTGGCATGCAGTGGACCTCATGCCAGCCCATTTTATGACTATTTAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGAGCAGCTGTTGTTGTTTCTGAAAGAATCTTGAGGGTGTTTGGAGTCTCAGAATGGCTTCCTTAAAGACTACCTTCAGACTCTCAGCTGCTCATCCACAACAGAGATCAGCCTTTCTTTGTAGATGATTCATTCCTGGCTGCATTTGAAAACCACATATTGTTAATTGCTTGACGAATTTAAATCCCTTGACTACTTTTCATTTCAGAAAACACTTACAAAAAAAGTCCAAATGAGGACCTTCCCTCCAGTGAATTAGCTGTGGCTTTCTCACAGTCCATAGTTAGGATAAATGTAAAGCCATTTCTCATTTTTCTCCGCACTTTCCAAGGGTACACTCCTTGTTTCCAAGATGGAATGAGAAATAAAGAAGTGCCCTTCCTGCCATCTTCTCCCCTGACCCTTTCCTCCTTCCCACTTTCCTCCTATTCCTCCCCAAACATGATTTATTTCTGCGTTTTGCAACTCTTGAGTTCTCAGCATTTAGTAAATGGTGTTGGTCCCTGTTGATTCCTTCCTCTCCTGGACCATGGAAGGTAGTAGGCCTTTCAGAAATTTCAGGTAGCAGCCAAACCCCAGAAGAAGAGAAGGAACACAGAGACCTAGACCATGTGAGAACCTGAGGTGTGCAGCATTTACTTCACAGATTCGTCTAGCATATTTGAGAGGTG

SEQ ID NO: 5 corresponds to the nucleotide sequence of transcript AR V4.Most of the upstream sequence common to all androgen receptors,corresponding to nucleotide 1-2822 of SEQ ID NO: 34, is not included.The first nucleotide of the variant specific sequences is shaded.

SEQ ID NO: 6 TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTCTTCTTCAAAAGAGCCGCTGAAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGA

GATTTTTCAGAATGAAC AAATTAAAAGAATCATCAGACACTAACCCCAAGCCATACTGCATGGCAGCACCAATGGGACTGACAGAAAACAACAGAAATAGGAAGAAATCCTACAGAGAAACAAACTTGAAAGCTGTCTCATGGCCTTTGAATCATACTTAAGTTTTATGATGGAAGGATACGACTATGAAGAAAGACACAGAGCAACATCAGACAGTCAAGAATTTCAGAGCCAGCTGGCATGCAGTGGACCTCATGCCAGCCCATTTTATGACTATTTAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGAGCAGCTGTTGTTGTTTCTGAAAGAATCTTGAGGGTGTTTGGAGTCTCAGAATGGCTTCCTTAAAGACTACCTTCAGACTCTCAGCTGCTCATCCACAACAGAGATCAGCCTTTCTTTGTAGATGATTCATTCCTGGCTGCATTTGAAAACCACATATTGTTAATTGCTTGACGAATTTAAATCCCTTGACTACTTTTCATTTCAGAAAACACTTACAAAAAAAGTCCAAATGAGGACCTTCCCTCCAGTGAATTAGCTGTGGCTTTCTCACAGTCCATAGTTAGGATAAATGTAAAGCCATTTCTCATTTTTCTCCGCACTTTCCAAGGGTACACTCCTTGTTTCCAAGATGGAATGAGAAATAAAGAAGTGCCCTTCCTGCCATCTTCTCCCCTGACCCTTTCCTCCTTCCCACTTTCCTCCTATTCCTCCCCAAACATGATTTATTTCTGCGTTTTGCAACTCTTGAGTTCTCAGCATTTAGTAAATGGTGTTGGTCCCTGTTGAT

CCTTCC TCTCCTGGACCATGGAAGGTAGTAGGCCTTTCAGAAATTTCAGGTAGCAGCCAAACCCCAGAAGAAGAGAAGGAACACAGAGACCTAGACCATGTGAGAACCTGAGGTGTGCAGCATTTACTTCACAGATTCGTCTAGCATATTTGAGAG GTG

SEQ ID NO: 6 corresponds to the nucleotide sequence of transcript AR V5.Most of the upstream sequence common to all androgen receptors,corresponding to nucleotide 1-2883 of SEQ ID NO: 34, is not included.The first nucleotide of the variant specific sequences is shaded.

SEQ ID NO: 7 GGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGC AGGGATGACTCTGGGA

ACTAGAATTCCAAAGACCCTCAGGCTGGTGATGCAAGTGGGAAGTCTCATTTCTGAGAAGTGCTGCTTCCTACCCACAATTCTTTGATAGCTGAGTGCTTTAGCTGATCTGCATAACTGAGGTGTGCACCAAGGAGCAGAATTACTCTATAAATTTTGGCATCAACATGTGCAACTTGTGACTCAGCACTTTGAAACTCTGGGGATTTTTTTGTTTGGTTGGTTTTTGTTTTAAGATGTCCTGTGGTATAGTGGAAATAGTACAATAGACTCAGATACAGAGAGGCCTTGTTTCTAGTCTTGGTTCTGTCACTTACTATCTTGATGTCCTTGCACAAATCACCAGACCTCTCTGAGCCTCAGTTTCTCCAACCACACTGTGGGAATAATAAAATCTTTTTTACGGCATTGTTGTAAGTATGCAGAGAAACTGGTACACAGTAGCCACACAATCAATGTCACCGTACCCTTCAGCCCTTCTTTTGTGGATGAAAAATGGTCTTTGTGCTCCCAGTCACCACTGGGGTCTGTTCTCTCTCTCTCTGCTGTTACAGTGTGGCTTTGGTTCTTGTTTCTTTGTTCTTTGGTCTGTAAATTACCCTTGAAACAACCCTTGAAATTTCCACTCCATGACCTAAATCGTCATCCCTAAATTGGTTACATACATATTTGGTGACACTTTGGAGGGGAAAAGCTTTATGTCTCTCTAACGTGTAGTTCTTAAGGGAATTTGCATATGGAAAAAACAGAGACTGCGTCTCTTAATTCCTCC

SEQ ID NO: 7 corresponds to the nucleotide sequence of transcript AR V6.Most of the upstream sequence common to all androgen receptors,corresponding to nucleotide 1-2883 of SEQ ID NO: 34, is not included.The first nucleotide of the variant specific sequences is shaded.

SEQ ID NO: 39 GGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGC AGGGATGACTCTGGGA

CAGGCAGCAGAGTGTCATAAAGAATTAACAACGTGGAACTCAGTTACTGGGATTTCTTCCATTCTCCTTTGATTCTCTAGACTAGAATTCCAAAGACCCTCAGGCTGGTGATGCAAGTGGGAAGTCTCATTTCTGAGAAGTGCTGCTTCCTACCCACAATTCTTTGATAGCTGAGTGCTTTAGCTGATCTGCATAACTGAGGTGTGCACCAAGGAGCAGAATTACTCTATAAATTTTGGCATCAACATGTGCAACTTGTGACTCAGCACTTTGAAACTCTGGGGATTTTTTTGTTTGGTTGGTTTTTGTTTTAAGATGTCCTGTGGTATAGTGGAAATAGTACAATAGACTCAGATACAGAGAGGCCTTGTTTCTAGTCTTGGTTCTGTCACTTACTATCTTGATGTCCTTGCACAAATCACCAGACCTCTCTGAGCCTCAGTTTCTCCAACCACACTGTGGGAATAATAAAATCTTTTTTACGGCATTGTTGTAAGTATGCAGAGAAACTGGTACACAGTAGCCACACAATCAATGTCACCGTACCCTTCAGCCCTTCTTTTGTGGATGAAAAATGGTCTTTGTGCTCCCAGTCACCACTGGGGTCTGTTCTCTCTCTCTCTGCTGTTACAGTGTGGCTTTGGTTCTTGTTTCTTTGTTCTTTGGTCTGTAAATTACCCTTGAAACAACCCTTGAAATTTCCACTCCATGACCTAAATCGTCATCCCTAAATTGGTTACATACATATTTGGTGACACTTTGGAGGGGAAAAGCTTTATGTCTCTCTAACGTGTAGTTCTTAAGGGAATTTGCATATGGAAAAAACAGAGACTGCGTCTCTTAATTCCTCC

SEQ ID NO: 39 corresponds to the nucleotide sequence of transcript ARV8. Most of the upstream sequence common to all androgen receptors,corresponding to nucleotide 1-2822 of SEQ ID NO: 34, is not included.The first nucleotide of the variant specific sequences is shaded.

TGTCACTATGGAGCTCTCACATGTGGAAGCTGCAAGGTCTTCTTCAAAAGAGCCGCTGAAGGGAAACAGAAGTACCTGTGCGCCAGCAGAAATGATTGCACTATTGATAAATTCCGAAGGAAAAATTGTCCATCTTGTCGTCTTCGGAAATGTTATGAAGCAGGGATGACTCTGGGA

ACAACTTACCTGAGCAA GCTGCTTTTTGGAGACATTTGCACATCTTTTGGGATCACGTTGTTAAGAAGTAGAACTAAGGGAAAAACACGCAGCCACCCAGAAATCGGTAGAGCCTTCAGCTCATCTGTTATTAATATTTCTGTGACAACAGATATCTAGGAAGTAAACAGGAAATTGCATCGCTATCCTGCATCACCTTTTTTGGAATCAGGTTCCATTCTTCTCAGTCCAGTTCAACCTTGTGATACTTTTTAGATCTCAACCAAGGCATAGAAATATATTTTCCCTTGCTTAATACCCCATGGAACCAATGCCCCTGTGGTTGAAGTAAAAATTGATTGTTGAGGGACATTTCAGCCCTCTAGCAGTCAACAATTAAAAACATGTAAGCACCGAGCACCTGCAGAAAACTTGGACTGGCATTTGGATCTAAGAAGAAAATCTGCATCTTGACCAAGATGAAAAGTCACCAGCCCAAGCTTGTGCAGTGAAGTGTCATGTTGGCCACAATGAAACTGAAAGAGACTGATGACTCTCCTCAGGGTGGAAAATGAGGCATGGAAGCTTTGATTAGTGAGCTGTTAGGCACACAGACATTAATTTCAAAGCATTCTCATCTCCAGTCTGAGTAATAATGCTTATAGTATTATGCAATTGTTTGGCTGCTGCAAGAAATTCAGCAGACTCCAACAAGTAGTCTTTCTTGGTCTCTGAGTGACTGTAACTTAAATTCTACCTCCCTTCTCTTCTCCTACATCTTCTCACTCCCCACCCCACCCCCACATACACACAATTCTTGTCCACTATGTTCAGAGAGATGCACGCACACATATATATGTATATATATAGTATATTTGTCAATAAAGCAGAAAAGAAGAAAAAACTCCAAGTAAACAATTTTCCATTTCCCCATCTCACTTCTGTCTTACAAGTGGATAGGAAAAGAAAAACCCCCAGTAAAAAATGGCAACCGCCCACCTCCCCAACTTTACATGCTGCTTCCTATGTTAGAGGATCTGTCTTAGGCATCTGATTATGGAGCCTGCTAGATACAAGCCCGTATTTAGACTGCTACAGTCAACAATGTCTCTCTTTCATACTAGAAAAATTCC

In certain examples, the androgen receptor variant nucleic acidcomprises SEQ ID NO: 1, or fragments thereof. In other examples, theandrogen receptor variant nucleic acid comprises SEQ ID NO: 39. In otherexamples, the androgen receptor variant nucleic acid comprises SEQ IDNO: 2.

In certain examples, the androgen receptor variant polypeptide comprisesa sequence selected from one or more of SEQ ID NO: 8, SEQ ID NO: 40, SEQID NO: 9, SEQ ID NO: 10, SEQ ID NO; 11, SEQ ID NO; 12, SEQ ID NO: 13 andSEQ ID NO: 14 or fragments thereof. The sequences are shown below:

SEQ ID NO: 8

SEQ ID NO: 8 corresponds to the AR-V7 protein sequence. In SEQ ID NO: 8,most of the n-terminal AR NTD and AR DBD sequences common to all ARproteins (amino acid 1-569 of SEQ ID NO: 35) are not included. The boldsequence corresponds to amino acids encoded by exon 2, the underlinedsequence corresponds to amino acids encoded by exon 3, followed byvariant specific sequence in italics.

SEQ ID NO: 9 C H Y G A L T C G S C K V F F K R A A E  G K O K YL C A S R N D C T I D K F R R K N C P S C R L R KC Y E A G M T L G E K F R V G N C K H L K M T R P Stop

SEQ ID NO: 9 corresponds to the AR-V1 protein sequence. In SEQ ID NO: 9,most of the N-terminal AR NTD and AR DBD sequences common to all ARproteins (amino acid 1-569 of SEQ ID NO: 35) are not included. The boldsequence corresponds to amino acids encoded by exon 2, the underlinedsequence corresponds to amino acids encoded by exon 3, followed byvariant specific sequence in italics.

SEQ ID NO: 10 C H Y G A L T C G S C K V F F K R A A E  G K Q K YL C A S R N D C T I D K F R R K N C P S C R L R K c Y E A G M T L G A V V V S E R I L R V F G V S E W L P Stop

SEQ ID NO: 10 corresponds to the AR-V2 protein sequence. In SEQ ID NO:10, most of the n-terminal AR NTD and AR DBD sequences common to all ARproteins (amino acid 1-569 of SEQ ID NO: 35) are not included. The boldsequence corresponds to amino acids encoded by exon 2, the underlinedsequence corresponds to amino acids encoded by exon 3, followed byvariant specific sequence in italics. Peptide sequences encoded by exon3 are duplicated.

SEQ ID NO: 11 C H Y G A L T C G S C K V F F K R A A E  G K Q K YL C A S R N D C T I D K F R R K N C P S C R L R Kc Y E A G M T L G G K Q K Y L C A S R N D C T I DK F R R K N C P S C R L R K C Y E A G M T L G  A VV V S E R I L R V F G V S E W L P Stop

SEQ ID NO: 11 corresponds to the AR-V3 protein sequence. In SEQ ID NO:11, most of the n-terminal AR NTD and AR DBD sequences common to all ARproteins (amino acid 1-569 of SEQ ID NO: 35) are not included. The firstamino acid of the variant specific sequence is shaded. The bold sequencecorresponds to amino acids encoded by exon 2, followed by variantspecific sequence in italics.

SEQ ID NO: 12 C H Y G A L T C G S C K V F F K R A A E G F F R MN K L K E S S D T N P K P Y C M A A P M G L T E NN R N R K K S Y R E T N L K A V S W P L N H T Stop

SEQ ID NO: 12 corresponds to the AR-V4 protein sequence. In SEQ ID NO:12, most of the n-terminal AR NTD and AR DBD sequences common to all ARproteins (amino acid 1-569 of SEQ ID NO: 35) are not included. The boldsequence corresponds to amino acids encoded by exon 2, the underlinedsequence corresponds to amino acids encoded by exon 3, followed byvariant specific sequence in italics.

SEQ ID NO: 13 C H Y G A L T C G S C K V F F K R A A E G K Q K YL C A S R N D C T I D K F R R K N C P S C R L R K C Y E A G M T L G G F F R M N K L K E S S D T N PK P Y C M A A P M G L T E N N R N R K K S Y R ET N L K A V S W P L N H T Stop

SEQ ID NO: 13 corresponds to the AR-V5 protein sequence. In SEQ ID NO:13 most of the n-terminal AR NTD and AR DBD sequences common to all ARproteins (amino acid 1-589 of SEQ ID NO: 35) are not included.Underlined sequence corresponds to amino acids encoded by exon 3,followed by variant specific sequence in italics.

SEQ ID NO: 14 G K O K Y L C A S R N D C T I D K F R R K N C P SC R L R K C Y E A G M T L G D Stop

SEQ ID NO: 14 corresponds to AR-V6 protein sequence. In SEQ ID NO: 14.most of the n-terminal AR NTD and AR DBD sequences common to all ARproteins (amino acid 1-589 of SEQ ID NO: 35) are not included.Underlined sequence corresponds to amino acids encoded by exon 3,followed by variant specific sequence in italics.

SEQ ID NO: 40 G K Q K Y L C A S R N D C T I D K F R R K N C P SC R L R K C Y E A G M T L G A G S R V S Stop

SEQ ID NO: 40 corresponds to the AR-V8 protein sequence. In SEQ ID NO:40, most of the n-terminal AR NTD and AR DBD sequences common to all ARproteins (amino acid 1-569 of SEQ ID NO: 35) are not included. The boldsequence corresponds to amino acids encoded by exon 2, the underlinedsequence corresponds to amino acids encoded by exon 3, followed byvariant specific sequence in italics.

C H Y G A L T C G S C K V F F K R A A E G K Q K YL C A S R N D C T I D K F R R K N C P S C R L R K C Y E A G M T L G D N L P E Q A A F W R H L H I F W D H V V K K StopDiagnostics and Prognostics

Prostate cancer depends on androgenic signaling for growth and survival.Androgens exert their cellular and physiologic effects through bindingto the androgen receptor. It is a finding of the present invention thatcertain prostate cancer cells express higher levels of androgen receptorvariants, in particular AR-V I-AR-V7 than corresponding normal tissues.Accordingly, expression levels of an androgen receptor variant nucleicacid molecule or polypeptide are correlated with a particular androgenrelated disease state (e.g., prostate cancer), and thus are useful indiagnosis. Accordingly, the present invention provides a number ofdiagnostic assays that are useful for the identification orcharacterization of an androgen related disease or disorder, e.g.prostate cancer.

In embodiments of the invention, a patient having an androgen relateddisease or disorder, e.g. prostate cancer, will show an increase in theexpression of an androgen receptor variant nucleic acid molecule.Alterations in gene expression are detected using methods known to theskilled artisan and described herein. Such information can be used todiagnose a androgen related disease or disorder, e.g. prostate cancer.In another embodiment, an alteration in the expression of an androgenreceptor variant nucleic acid molecule is detected using polymerasechain reaction (PCR), for example, real time PCR or semi quantitativereal time PCR to detect changes in gene expression.

Primers used for amplification of an androgen receptor variant nucleicacid molecule, including but not limited to those primer sequencesdescribed herein, are useful in diagnostic methods of the invention. Theprimers of the invention embrace oligonucleotides of sufficient lengthand appropriate sequence so as to provide specific initiation ofpolymerization on a significant number of nucleic acids. Specifically,the term “primer” as used herein refers to a sequence comprising two ormore deoxyribonucleotides or ribonucleotides, preferably more thanthree, and most preferably more than 8, which sequence is capable ofinitiating synthesis of a primer extension product, which issubstantially complementary to a locus strand. The primer must besufficiently long to prime the synthesis of extension products in thepresence of the inducing agent for polymerization. The exact length ofprimer will depend on many factors, including temperature, buffer, andnucleotide composition. Primers of the invention are designed to be“substantially” complementary to each strand of the genomic locus to beamplified and include the appropriate G or C nucleotides as discussedabove. This means that the primers must be sufficiently complementary tohybridize with their respective strands under conditions that allow theagent for polymerization to perform. In other words, the primers shouldhave sufficient complementarity with the 5′ and 3′ flanking sequences tohybridize therewith and permit amplification of the genomic locus. Whileexemplary primers are provided herein, it is understood that any primerthat hybridizes with the target sequences of the invention are useful inthe method of the invention for detecting androgen receptor variantnucleic acid molecules.

Exemplary primer sets useful in the invention are shown below:

(P1): (SEQ ID NO: 15) TGTCACTATGGAGCTCTCACATGTGG and (SEQ ID NO: 16)CACCTCTCAAATATGCTAGACGAATCTGT; (P2) (SEQ ID NO: 17)TGTCACTATGGAGCTCTCACATGTGG and (SEQ ID NO: 18)GTACTCATTCAAGTATCAGATATGCGGTATCAT; (P3) (SEQ ID NO: 19)TGTCACTATGGAGCTCTCACATGTGG and (SEQ ID NO: 20)CTGTGGATCAGCTACTACCTTCAGCTC; (P4) (SEQ ID NO: 21)GTTGCTCCCGCAAGTTTCCTTCTC and (SEQ ID NO: 22)CTGTTGTGGATGAGCAGCTGAGAGTCT; (P5) (SEQ ID NO: 23)GTTGCTCCCGCAAGTTTCCTTCTC and (SEQ ID NO: 24) TTTGAATGAGGCAAGTCAGCCTTTCT;(P6) (SEQ ID NO: 25) CCATCTTGTCGTCTTCGGAAATGTTATGAAGC and(SEQ ID NO: 26) CTGTTGTGGATGAGCAGCTGAGAGTCT; (P7) (SEQ ID NO: 27)CCATCTTGTCGTCTTCGGAAATGTTATGAAGC and (SEQ ID NO: 28)TTTGAATGAGGCAAGTCAGCCTTTCT; (P8) (SEQ ID NO: 29)CCATCTTGTCGTCTTCGGAAATGTTATGAAGC and (SEQ ID NO: 30)AGCTTCTGGGTTGTCTCCTCAGTGG; and (P9) (SEQ ID NO: 37)Tgtcactatggagctctcacatgtgg and (SEQ ID NO: 38) Cattgtggccaacatgacacttca.

In one embodiment, androgen receptor variant-specific primers amplify adesired genomic target using the polymerase chain reaction (PCR), inparticular semi quantitative RT-PCR. The amplified product is thendetected using standard methods known in the art. In one embodiment, aPCR product (i.e., amplicon) or real-time PCR product is detected byprobe binding. In one embodiment, probe binding generates a fluorescentsignal, for example, by coupling a fluorogenic dye molecule and aquencher moiety to the same or different oligonucleotide substrates(e.g., TaqMan® (Applied Biosystems, Foster City, Calif., USA), MolecularBeacons (see, for example, Tyagi et al., Nature Biotechnology14(3):303-8, 1996), Scorpions® (Molecular Probes Inc., Eugene, Oreg.,USA)). In another example, a PCR product is detected by the binding of afluorogenic dye that emits a fluorescent signal upon binding (e.g.,SYBR® Green (Molecular Probes)). Such detection methods are useful forthe detection of an androgen receptor variant PCR product.

In another embodiment, hybridization with PCR probes that are capable ofdetecting an androgen receptor variant nucleic acid molecule, includinggenomic sequences, or closely related molecules, may be used tohybridize to a nucleic acid sequence derived from a patient having anandrogen related disease or disorder, e.g. prostate cancer. Thespecificity of the probe determines whether the probe hybridizes to anaturally occurring sequence, allelic variants, or other relatedsequences. Hybridization techniques may be used to identify mutationsindicative of a androgen related disease or disorder, e.g. prostatecancer, or may be used to monitor expression levels of these genes (forexample, by Northern analysis (Ausubel et al., supra).

The invention features methods of determining if a subject will respondto androgen therapy, the method comprising determining the level ofexpression or biological activity of an androgen receptor variantpolypeptide in a subject sample wherein an alteration in the level ofexpression or biological activity relative to the expression orbiological activity in a reference indicates that the subject willrespond to androgen therapy.

The invention also features methods of determining if a subject willrespond to androgen therapy, the method comprising determining the levelof expression or biological activity of an androgen receptor variantnucleic acid in a subject sample wherein an alteration in the level ofexpression relative to the expression in a reference indicates that thesubject will respond to androgen therapy.

In preferred embodiments, the subject has prostate cancer. In otherembodiments, the subject is in remission from prostate cancer.

In certain embodiments the invention features diagnostic methods. Forexample a subject, for example a patient, may be diagnosed for apropensity to develop a androgen related disease or disorder, e.g.prostate cancer, by direct analysis of the sequence of an androgenreceptor variant nucleic acid molecule. The sequence of an androgenreceptor variant nucleic acid molecule derived from a subject iscompared to a reference sequence. An alteration in the sequence of theandrogen receptor variant nucleic acid molecule relative to thereference indicates that the patient has or has a propensity to developan androgen related disease or disorder, e.g. prostate cancer.

In another approach, diagnostic methods of the invention are used toassay the expression of an androgen receptor variant polypeptide in abiological sample relative to a reference (e.g., the level of androgenreceptor variant polypeptide present in a corresponding control sample,or in a sample taken before a treatment, such as surgical treatment). Inone embodiment, the level of an androgen receptor variant polypeptide isdetected using an antibody that specifically binds an androgen receptorvariant polypeptide. Exemplary antibodies that specifically bind anandrogen receptor variant polypeptide are described herein. Suchantibodies are useful for the diagnosis of an androgen related diseaseor disorder. Methods for measuring an antibody-androgen receptor variantcomplex include, for example, detection of fluorescence, luminescence,chemiluminescence, absorbance, reflectance, transmittance, birefringenceor refractive index. Optical methods include microscopy (both confocaland non-confocal), imaging methods and non-imaging methods. Methods forperforming these assays are readily known in the art. Useful assaysinclude, for example, an enzyme immune assay (EIA) such as enzyme-linkedimmunosorbent assay (ELISA), a radioimmune assay (RIA), a Western blotassay, or a slot blot assay. These methods are also described in, e.g.,Methods in Cell Biology: Antibodies in Cell Biology, volume 37 (Asai,ed. 1993); Basic and Clinical Immunology (Stites & Terr, eds., 7th ed.1991); and Harlow & Lane, supra. Immunoassays can be used to determinethe quantity of androgen receptor variant in a sample, where an increasein the level of the androgen receptor variant polypeptide is diagnosticof a patient having an androgen related disease or disorder, e.g.prostate cancer.

In general, the measurement of an androgen receptor variant polypeptideor nucleic acid molecule in a subject sample is compared with adiagnostic amount present in a reference. A diagnostic amountdistinguishes between a diseased tissue or, for example a neoplastictissue, and a control tissue. The skilled artisan appreciates that theparticular diagnostic amount used can be adjusted to increasesensitivity or specificity of the diagnostic assay depending on thepreference of the diagnostician. In general, any significant increase(e.g., at least about 10%, 15%, 30%, 50%, 60%, 75%, 80%, or 90%) in thelevel of an androgen receptor variant polypeptide or nucleic acidmolecule in the subject sample relative to a reference may be used todiagnose an androgen related disease or disorder, e.g. prostate cancer.In one embodiment, the reference is the level of androgen receptorvariant polypeptide or nucleic acid molecule present in a control sampleobtained from a patient that does not have an androgen related diseaseor disorder, e.g. prostate cancer. In another embodiment, the referenceis the level of androgen receptor variant polypeptide or nucleic acidmolecule present in a control sample obtained from subjects with adisease of less severity, e.g., early stage non-aggressive prostatecancer. In another embodiment, the reference is a baseline level ofandrogen receptor variant present in a biologic sample derived from apatient prior to, during, or after treatment for an androgen relateddisease or disorder, e.g. prostate cancer. In yet another embodiment,the reference is a standardized curve.

Types of Biological Samples

The level of an androgen receptor variant polypeptide or nucleic acidmolecule can be measured in different types of biologic samples. In oneembodiment, the biologic sample is a tissue sample that includes cellsof a tissue or organ. Such tissue is obtained, for example, from abiopsy. In another embodiment, the biologic sample is a biologic fluidsample (e.g., blood, blood plasma, serum, urine, seminal fluids,ascites, or cerebrospinal fluid).

In certain exemplary embodiments, the sample is from prostate.

In other certain exemplary embodiments, the sample is from a subjectundergoing treatment for prostate cancer.

Patient Monitoring

The disease state or treatment of a patient having prostate cancer canbe monitored using the methods and compositions of the invention. In oneembodiment, a microarray is used to assay the expression profile ofandrogen receptor variant nucleic acid molecule. Such monitoring may beuseful, for example, in assessing response of a patient to androgentherapy, in assessing the remission status of a patient, or in assessingthe response of a particular drug in a patient.

Therapeutics that alter the expression of an androgen receptor variantnucleic acid molecule or androgen receptor variant polypeptide (e.g., anandrogen receptor variant, for example AR-V1, AR-V2, AR-V3, AR-V4,AR-V5, AR-V6, AR-V7, AR-V8, or fragments thereof), may be useful in theinvention.

Kits

The invention also provides kits for the diagnosis or monitoring of anandrogen related disease or disorder, e.g. prostate cancer, in abiological sample obtained from a subject. In one embodiment, the kitdetects an increase in the expression of an androgen receptor variantnucleic acid molecule or polypeptide relative to a reference level ofexpression. In another embodiment, the kit detects an alteration in thesequence of an androgen receptor variant nucleic acid molecule derivedfrom a subject relative to a reference sequence. In related embodiments,the kit includes reagents for monitoring the expression of an androgenreceptor variant nucleic acid molecule, such as primers or probes thathybridize to an androgen receptor variant nucleic acid molecule. Inother embodiments, the kit includes an antibody that binds to anandrogen receptor variant polypeptide.

Optionally, the kit includes directions for monitoring an androgenreceptor variant nucleic acid molecule or polypeptide levels in abiological sample derived from a subject. In other embodiments, the kitcomprises a sterile container which contains the primer, probe,antibody, or other detection regents; such containers can be boxes,ampules, bottles, vials, tubes, bags, pouches, blister-packs, or othersuitable container form known in the art. Such containers can be made ofplastic, glass, laminated paper, metal foil, or other materials suitablefor holding nucleic acids. The instructions will generally includeinformation about the use of the primers or probes described herein andtheir use in diagnosing an androgen related disease or disorder, e.g.prostate cancer. Preferably, the kit further comprises any one or moreof the reagents described in the diagnostic assays described herein. Inother embodiments, the instructions include at least one of thefollowing: description of the primer or probe; methods for using theenclosed materials for the diagnosis of an androgen related disease ordisorder, e.g. prostate cancer; precautions; warnings; indications;clinical or research studies; and/or references. The instructions may beprinted directly on the container (when present), or as a label appliedto the container, or as a separate sheet, pamphlet, card, or foldersupplied in or with the container.

Androgen Receptor Variant Antibodies

Antibodies are well known to those of ordinary skill in the science ofimmunology. As used herein, the term “antibody” means not only intactantibody molecules, but also fragments of antibody molecules that retainimmunogen binding ability. Such fragments are also well known in the artand are regularly employed both in vitro and in vivo. Accordingly, asused herein, the term “antibody” means not only intact immunoglobulinmolecules but also the well-known active fragments F(ab′)₂, and Fab.F(ab′)₂, and Fab fragments which lack the Fc fragment of intactantibody, clear more rapidly from the circulation, and may have lessnon-specific tissue binding of an intact antibody (Wahl et al., J. Nucl.Med. 24:316-325 (1983). The antibodies of the invention comprise wholenative antibodies, bispecific antibodies; chimeric antibodies; Fab,Fab′, single chain V region fragments (scFv) and fusion polypeptides.

In one embodiment, an antibody that binds an androgen receptor variantpolypeptide (e.g., an androgen receptor variant, for example AR-V1,AR-V2, AR-V3, AR-V4, AR-V5, AR-V6, AR-V7, AR-V8 or fragments thereof) ismonoclonal. Alternatively, the antiandrogen receptor variant antibody isa polyclonal antibody. The preparation and use of polyclonal antibodiesare also known the skilled artisan. The invention also encompasseshybrid antibodies, in which one pair of heavy and light chains isobtained from a first antibody, while the other pair of heavy and lightchains is obtained from a different second antibody. Such hybrids mayalso be formed using humanized heavy and light chains. Such antibodiesare often referred to as “chimeric” antibodies.

In general, intact antibodies are said to contain “Fc” and “Fab”regions. The Fc regions are involved in complement activation and arenot involved in antigen binding. An antibody from which the Fc′ regionhas been enzymatically cleaved, or which has been produced without theFc′ region, designated an “F(ab′)₂” fragment, retains both of theantigen binding sites of the intact antibody. Similarly, an antibodyfrom which the Fc region has been enzymatically cleaved, or which hasbeen produced without the Fc region, designated an “Fab′” fragment,retains one of the antigen binding sites of the intact antibody. Fab′fragments consist of a covalently bound antibody light chain and aportion of the antibody heavy chain, denoted “Fd.” The Fd fragments arethe major determinants of antibody specificity (a single Fd fragment maybe associated with up to ten different light chains without alteringantibody specificity). Isolated Fd fragments retain the ability tospecifically bind to immunogenic epitopes.

Antibodies can be made by any of the methods known in the art utilizingandrogen receptor variant polypeptides unique to each of the variants(e.g., an androgen receptor variant, for example AR-V1, AR-V2, AR-V3,AR-V4, AR-V5, AR-V6, AR-V7, AR-V8, or fragments thereof), or immunogenicfragments thereof, as an immunogen. One method of obtaining antibodiesis to immunize suitable host animals with an immunogen and to followstandard procedures for polyclonal or monoclonal antibody production.The immunogen will facilitate presentation of the immunogen on the cellsurface. Immunization of a suitable host can be carried out in a numberof ways. Nucleic acid sequences encoding an androgen receptor variantpolypeptide (e.g., an androgen receptor variant, for example AR-V1,AR-V2, AR-V3, AR-V4, AR-V5, AR-V6, AR-V7, or fragments thereof), orimmunogenic fragments thereof, can be provided to the host in a deliveryvehicle that is taken up by immune cells of the host. The cells will inturn express the receptor on the cell surface generating an immunogenicresponse in the host. Alternatively, nucleic acid sequences encoding anandrogen receptor variant polypeptide (e.g., an androgen receptorvariant, for example AR-V1, AR-V2, AR-V3, AR-V4, AR-V5, AR-V6, AR-V7,AR-V-8 or fragments thereof), or immunogenic fragments thereof, can beexpressed in cells in vitro, followed by isolation of the receptor andadministration of the receptor to a suitable host in which antibodiesare raised.

Using either approach, antibodies can then be purified from the host.Antibody purification methods may include salt precipitation (forexample, with ammonium sulfate), ion exchange chromatography (forexample, on a cationic or anionic exchange column preferably run atneutral pH and eluted with step gradients of increasing ionic strength),gel filtration chromatography (including gel filtration HPLC), andchromatography on affinity resins such as protein A, protein G,hydroxyapatite, and anti-immunoglobulin.

Antibodies can be conveniently produced from hybridoma cells engineeredto express the antibody. Methods of making hybridomas are well known inthe art. The hybridoma cells can be cultured in a suitable medium, andspent medium can be used as an antibody source. Polynucleotides encodingthe antibody of interest can in turn be obtained from the hybridoma thatproduces the antibody, and then the antibody may be producedsynthetically or recombinantly from these DNA sequences. For theproduction of large amounts of antibody, it is generally more convenientto obtain an ascites fluid. The method of raising ascites generallycomprises injecting hybridoma cells into an immunologically naivehistocompatible or immunotolerant mammal, especially a mouse. The mammalmay be primed for ascites production by prior administration of asuitable composition; e.g., Pristane.

Monoclonal antibodies (Mabs) produced by methods of the invention can be“humanized” by methods known in the art. “Humanized” antibodies areantibodies in which at least part of the sequence has been altered fromits initial form to render it more like human immunoglobulins.Techniques to humanize antibodies are particularly useful when non-humananimal (e.g., murine) antibodies are generated. Examples of methods forhumanizing a murine antibody are provided in U.S. Pat. Nos. 4,816,567,5,530,101, 5,225,539, 5,585,089, 5,693,762 and 5,859,205.

In certain preferred embodiments, the antibody specifically binds to anandrogen receptor variant-7 (AR-V7) protein. In other embodiments, theantibody specifically binds to an androgen receptor variant-1 (AR-V1)protein. In other certain preferred embodiments, the antibodyspecifically binds to an androgen receptor variant-8 (AR-V8) protein.

Preferably, the antibody binds to a CKHLKMRP epitope of an AR-V7polypeptide, corresponding to SEQ ID NO: 33.

Androgen Receptor Variant Polypeptide Expression

In general, androgen receptor variant polypeptides, variants, andfragments thereof may be produced by transformation of a suitable hostcell with all or part of a polypeptide-encoding nucleic acid molecule orfragment thereof in a suitable expression vehicle.

Those skilled in the field of molecular biology will understand that anyof a wide variety of expression systems may be used to provide therecombinant protein. The precise host cell used is not critical to theinvention. A polypeptide of the invention may be produced in aprokaryotic host (e.g., E. coli) or in a eukaryotic host (e.g.,Saccharomyces cerevisiae, insect cells, e.g., Sf21 cells, or mammaliancells, e.g., NIH 3T3, HeLa, or preferably COS cells). Such cells areavailable from a wide range of sources (e.g., the American Type CultureCollection, Rockland, Md.; also, see, e.g., Ausubel et al., supra). Themethod of transformation or transfection and the choice of expressionvehicle will depend on the host system selected. Transformation andtransfection methods are described, e.g., in Ausubel et al. (supra);expression vehicles may be chosen from those provided, e.g., in CloningVectors: A Laboratory Manual (P. H. Pouwels et al., 1985, Supp. 1987).

A variety of expression systems exist for the production of thepolypeptides of the invention. Expression vectors useful for producingsuch polypeptides include, without limitation, chromosomal, episomal,and virus-derived vectors, e.g., vectors derived from bacterialplasmids, from bacteriophage, from transposons, from yeast episomes,from insertion elements, from yeast chromosomal elements, from virusessuch as baculoviruses, papova viruses, such as SV40, vaccinia viruses,adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses,and vectors derived from combinations thereof.

For example, one particular bacterial expression system for polypeptideproduction is the E. coli pET expression system (Novagen, Inc., Madison,Wis.). According to this expression system, DNA encoding a polypeptideis inserted into a pET vector in an orientation designed to allowexpression. Since the gene encoding such a polypeptide is under thecontrol of the T7 regulatory signals, expression of the polypeptide isachieved by inducing the expression of T7 RNA polymerase in the hostcell. This is typically achieved using host strains that express T7 RNApolymerase in response to IPTG induction. Once produced, recombinantpolypeptide is then isolated according to standard methods known in theart, for example, those described herein.

Another bacterial expression system for polypeptide production is thepGEX expression system (Pharmacia). This system employs a GST genefusion system that is designed for high-level expression of genes orgene fragments as fusion proteins with rapid purification and recoveryof functional gene products. The protein of interest is fused to thecarboxyl terminus of the glutathione S-transferase protein fromSchistosoma japonicum and is readily purified from bacterial lysates byaffinity chromatography using Glutathione Sepharose 4B. Fusion proteinscan be recovered under mild conditions by elution with glutathione.Cleavage of the glutathione S-transferase domain from the fusion proteinis facilitated by the presence of recognition sites for site-specificproteases upstream of this domain. For example, proteins expressed inpGEX-2T plasmids may be cleaved with thrombin; those expressed inpGEX-3X may be cleaved with factor Xa.

Once the recombinant polypeptide of the invention is expressed, it isisolated, e.g., using affinity chromatography. In one example, anantibody (e.g., produced as described herein) raised against apolypeptide of the invention may be attached to a column and used toisolate the recombinant polypeptide. Lysis and fractionation ofpolypeptide-harboring cells prior to affinity chromatography may beperformed by standard methods (see, e.g., Ausubel et al., supra).

Once isolated, the recombinant protein can, if desired, be furtherpurified, e.g., by high performance liquid chromatography (see, e.g.,Fisher, Laboratory Techniques In Biochemistry and Molecular Biology,eds., Work and Burdon, Elsevier, 1980). Polypeptides of the invention,particularly short peptide fragments, can also be produced by chemicalsynthesis (e.g., by the methods described in Solid Phase PeptideSynthesis, 2nd ed., 1984 The Pierce Chemical Co., Rockford, Ill.). Thesegeneral techniques of polypeptide expression and purification can alsobe used to produce and isolate useful peptide fragments or analogs(described herein).

Androgen Receptor Variant Polypeptides and Analogs

Also included in the invention are androgen receptor variantpolypeptides, variants, or fragments thereof containing at least onealteration relative to a reference sequence. Such alterations includecertain polymorphic variations, mutations, deletions, insertions, orpost-translational modifications. The invention further includes analogsof any naturally-occurring polypeptide of the invention. Analogs candiffer from naturally-occurring polypeptides of the invention by aminoacid sequence differences, by post-translational modifications, or byboth. Analogs of the invention will generally exhibit at least 85%, morepreferably 90%, and most preferably 95% or even 99% identity with all orpart of a naturally-occurring amino acid sequence of the invention. Thelength of sequence comparison is at least 10, 13, 15 amino acidresidues, preferably at least 25 amino acid residues, and morepreferably more than 35 amino acid residues. Again, in an exemplaryapproach to determining the degree of identity, a BLAST program may beused, with a probability score between e⁻³ and e−¹⁰⁰ indicating aclosely related sequence. Modifications include in vivo and in vitrochemical derivatization of polypeptides, e.g., acetylation,carboxylation, phosphorylation, or glycosylation; such modifications mayoccur during polypeptide synthesis or processing or following treatmentwith isolated modifying enzymes. Analogs can also differ from thenaturally-occurring polypeptides of the invention by alterations inprimary sequence. These include genetic variants, both natural andinduced (for example, resulting from random mutagenesis by irradiationor exposure to ethanemethylsulfate or by site-specific mutagenesis asdescribed in Sambrook, Fritsch and Maniatis, Molecular Cloning: ALaboratory Manual (2d ed.), CSH Press, 1989, or Ausubel et al., supra).Also included are cyclized peptides, molecules, and analogs whichcontain residues other than L-amino acids, e.g., D-amino acids ornon-naturally occurring or synthetic amino acids.

In addition to full-length polypeptides, the invention also includesfragments of any one of the polypeptides of the invention. As usedherein, the term “a fragment” means at least 5, 10, 13, or 15 aminoacids. In other embodiments a fragment is at least 20 contiguous aminoacids, at least 30 contiguous amino acids, or at least 50 contiguousamino acids, and in other embodiments at least 60 to 80 or morecontiguous amino acids. Fragments of the invention can be generated bymethods known to those skilled in the art or may result from normalprotein processing (e.g., removal of amino acids from the nascentpolypeptide that are not required for biological activity or removal ofamino acids by alternative mRNA splicing or alternative proteinprocessing events).

Androgen Receptor Variant Polynucleotides

In general, the invention includes any nucleic acid sequence encoding anandrogen receptor variant polypeptide (e.g., androgen receptor variant,for example AR-V1, AR-V2, AR-V3, AR-V4, AR-V5, AR-V6, AR-V7, AR-V8 orfragments thereof). Also included in the methods of the invention areany nucleic acid molecule containing at least one strand that hybridizeswith such a nucleic acid sequence (e.g., an inhibitory nucleic acidmolecule, such as a dsRNA, siRNA, shRNA, or antisense molecule). Anisolated nucleic acid molecule can be manipulated using recombinant DNAtechniques well known in the art. Thus, a nucleotide sequence containedin a vector in which 5′ and 3′ restriction sites are known, or for whichpolymerase chain reaction (PCR) primer sequences have been disclosed, isconsidered isolated, but a nucleic acid sequence existing in its nativestate in its natural host is not. An isolated nucleic acid may besubstantially purified, but need not be. For example, a nucleic acidmolecule that is isolated within a cloning or expression vector maycomprise only a tiny percentage of the material in the cell in which itresides. Such a nucleic acid is isolated, however, as the term is usedherein, because it can be manipulated using standard techniques known tothose of ordinary skill in the art.

Androgen Receptor Variant Polynucleotide Therapy

Polynucleotide therapy featuring a polynucleotide encoding an androgenreceptor variant protein, variant, or fragment thereof is anothertherapeutic approach for treating a androgen related disease ordisorder, e.g. prostate cancer. Such nucleic acid molecules can bedelivered to cells of a subject having an androgen related disease ordisorder, e.g. prostate cancer. The nucleic acid molecules must bedelivered to the cells of a subject in a form in which they can be takenup so that therapeutically effective levels of an androgen receptorvariant protein (e.g., androgen receptor variant, for example AR-V1,AR-V2, AR-V3, AR-V4, AR-V5, AR-V6, AR-V7, AR-V8 or fragments thereof) orfragment thereof can be produced.

Transducing viral (e.g., retroviral, adenoviral, and adeno-associatedviral) vectors can be used for somatic cell gene therapy, especiallybecause of their high efficiency of infection and stable integration andexpression (see, e.g., Cayouette et al., Human Gene Therapy 8:423-430,1997; Kido et al., Current Eye Research 15:833-844, 1996; Bloomer etal., Journal of Virology 71:6641-6649, 1997; Naldini et al., Science272:263-267, 1996; and Miyoshi et al., Proc. Natl. Acad. Sci. U.S.A.94:10319, 1997). For example, a polynucleotide encoding an androgenreceptor variant protein, variant, or a fragment thereof, can be clonedinto a retroviral vector and expression can be driven from itsendogenous promoter, from the retroviral long terminal repeat, or from apromoter specific for a target cell type of interest. Other viralvectors that can be used include, for example, a vaccinia virus, abovine papilloma virus, or a herpes virus, such as Epstein-Barr Virus(also see, for example, the vectors of Miller, Human Gene Therapy 15-14,1990; Friedman, Science 244:1275-1281, 1989; Eglitis et al.,BioTechniques 6:608-614, 1988; Tolstoshev et al., Current Opinion inBiotechnology 1:5561, 1990; Sharp, The Lancet 337:1277-1278, 1991;Cornetta et al., Nucleic Acid Research and Molecular Biology 36:311-322,1987; Anderson, Science 226:401-409, 1984; Moen, Blood Cells 17:407-416,1991; Miller et al., Biotechnology 7:980-990, 1989; Le Gal La Salle etal., Science 259:988-990, 1993; and Johnson, Chest 107:77S-83S, 1995).Retroviral vectors are particularly well developed and have been used inclinical settings (Rosenberg et al., N. Engl. J. Med 323:370, 1990;Anderson et al., U.S. Pat. No. 5,399,346). Most preferably, a viralvector is used to administer an androgen receptor variant polynucleotidesystemically.

Non-viral approaches can also be employed for the introduction oftherapeutic to a cell of a patient diagnosed as having an androgenrelated disease or disorder, e.g. prostate cancer. For example, anucleic acid molecule can be introduced into a cell by administering thenucleic acid in the presence of lipofection (Feigner et al., Proc. Natl.Acad. Sci. U.S.A. 84:7413, 1987; Ono et al., Neuroscience Letters17:259, 1990; Brigham et al., Am. J. Med. Sci. 298:278, 1989; Staubingeret al., Methods in Enzymology 101:512, 1983),asialoorosomucoid-polylysine conjugation (Wu et al., Journal ofBiological Chemistry 263:14621, 1988; Wu et al., Journal of BiologicalChemistry 264:16985, 1989), or by micro-injection under surgicalconditions (Wolff et al., Science 247:1465, 1990). Preferably thenucleic acids are administered in combination with a liposome andprotamine.

Gene transfer can also be achieved using non-viral means involvingtransfection in vitro. Such methods include the use of calciumphosphate, DEAE dextran, electroporation, and protoplast fusion.Liposomes can also be potentially beneficial for delivery of DNA into acell. Transplantation of normal genes into the affected tissues of apatient can also be accomplished by transferring a normal nucleic acidinto a cultivatable cell type ex vivo (e.g., an autologous orheterologous primary cell or progeny thereof), after which the cell (orits descendants) are injected into a targeted tissue.

cDNA expression for use in polynucleotide therapy methods can bedirected from any suitable promoter (e.g., the human cytomegalovirus(CMV), simian virus 40 (SV40), or metallothionein promoters), andregulated by any appropriate mammalian regulatory element. For example,if desired, enhancers known to preferentially direct gene expression inspecific cell types can be used to direct the expression of a nucleicacid. The enhancers used can include, without limitation, those that arecharacterized as tissue- or cell-specific enhancers. Alternatively, if agenomic clone is used as a therapeutic construct, regulation can bemediated by the cognate regulatory sequences or, if desired, byregulatory sequences derived from a heterologous source, including anyof the promoters or regulatory elements described above.

Another therapeutic approach included in the invention involvesadministration of a recombinant therapeutic, such as a recombinantandrogen receptor variant protein, variant, or fragment thereof, eitherdirectly to the site of a potential or actual disease-affected tissue orsystemically (for example, by any conventional recombinant proteinadministration technique). The dosage of the administered proteindepends on a number of factors, including the size and health of theindividual patient. For any particular subject, the specific dosageregimes should be adjusted over time according to the individual needand the professional judgment of the person administering or supervisingthe administration of the compositions.

Screening Assays

As reported herein, the expression of an androgen receptor variantpolypeptide is increased in neoplastic tissues, and in particularexamples in neoplastic tissues from patients with progressive diseases.Accordingly, compounds that modulate the expression or activity of anandrogen receptor variant polypeptide, variant, or fragment thereof areuseful in the methods of the invention for the treatment or preventionof an androgen related disease or disorder, such as prostate cancer, oradvanced prostate cancer. Any number of methods are available forcarrying out screening assays to identify such compounds. In oneapproach, candidate compounds are identified that specifically bind toand alter the activity of a polypeptide of the invention (e.g., anandrogen receptor variant activity). Methods of assaying such biologicalactivities are known in the art and are described herein. The efficacyof such a candidate compound is dependent upon its ability to interactwith an androgen receptor variant polypeptide, variant, or fragment.Such an interaction can be readily assayed using any number of standardbinding techniques and functional assays (e.g., those described inAusubel et al., supra). For example, a candidate compound may be testedin vitro for interaction and binding with a polypeptide of theinvention. Standard methods for perturbing or reducing androgen receptorvariant expression include mutating or deleting an endogenous androgenreceptor variant sequence, interfering with androgen receptor variantexpression using RNAi, or microinjecting an androgen receptorvariant-expressing cell with an antibody that binds androgen receptorvariant and interferes with its function.

Potential agonists and antagonists of an androgen receptor variantpolypeptide include organic molecules, peptides, peptide mimetics,polypeptides, nucleic acid molecules (e.g., double-stranded RNAs,siRNAs, antisense polynucleotides), and antibodies that bind to anucleic acid sequence or polypeptide of the invention and therebyinhibit or decrease its activity. Potential antagonists also includesmall molecules that bind to the androgen receptor variant polypeptidethereby preventing binding to cellular molecules with which the androgenreceptor variant polypeptide normally interacts, such that the normalbiological activity of the androgen receptor variant polypeptide isreduced or inhibited. Small molecules of the invention preferably have amolecular weight below 2,000 daltons, more preferably between 300 and1,000 daltons, and most preferably between 400 and 700 daltons. It ispreferred that these small molecules are organic molecules.

For example, a recombinant polypeptide of the invention may be purifiedby standard techniques from cells engineered to express the polypeptide(e.g., those described above) and may be immobilized on a column. Asolution of candidate compounds is then passed through the column, and acompound specific for the androgen receptor variant polypeptide isidentified on the basis of its ability to bind to the androgen receptorvariant polypeptide and be immobilized on the column. To isolate thecompound, the column is washed to remove non-specifically boundmolecules, and the compound of interest is then released from the columnand collected.

In one particular example, methods may be used to isolate a compoundbound to a polypeptide microarray. Compounds isolated by this method (orany other appropriate method) may, if desired, be further purified(e.g., by high performance liquid chromatography). In addition, thesecandidate compounds may be tested for their ability to alter thebiological activity of an androgen receptor variant polypeptide (e.g.,androgen receptor variant, for example AR-V1, AR-V2, AR-V3, AR-V4,AR-V5, AR-V6, AR-V7, AR-V8 or fragments thereof).

Any in vivo protein interaction detection system, for example, anytwo-hybrid assay may be utilized to identify compounds that interactwith an androgen receptor variant polypeptide. Interacting compoundsisolated by this method (or any other appropriate method) may, ifdesired, be further purified (e.g., by high performance liquidchromatography). Compounds isolated by any approach described herein maybe used as therapeutics to treat a androgen related disease or disorder,e.g. prostate cancer in a human patient.

In addition, compounds that inhibit the expression of an androgenreceptor variant nucleic acid molecule whose expression is increased ina patient having a androgen related disease or disorder, e.g. prostatecancer, are also useful in the methods of the invention. Any number ofmethods are available for carrying out screening assays to identify newcandidate compounds that alter the expression of an androgen receptorvariant nucleic acid molecule. In one working example, candidatecompounds are added at varying concentrations to the culture medium ofcultured cells expressing one of the nucleic acid sequences of theinvention. Gene expression is then measured, for example, by microarrayanalysis, Northern blot analysis (Ausubel et al., supra), or RT-PCR,using any appropriate fragment prepared from the nucleic acid moleculeas a hybridization probe. The level of gene expression in the presenceof the candidate compound is compared to the level measured in a controlculture medium lacking the candidate molecule. A compound that promotesan alteration in the expression of an androgen receptor variant gene, ora functional equivalent thereof, is considered useful in the invention;such a molecule may be used, for example, as a therapeutic to treat aandrogen related disease or disorder, e.g. prostate cancer in a humanpatient.

In another approach, the effect of candidate compounds is measured atthe level of polypeptide production to identify those that promote analteration in an androgen receptor variant polypeptide level. The levelof androgen receptor variant polypeptide can be assayed using anystandard method. Standard immunological techniques include Westernblotting or immunoprecipitation with an antibody specific for anandrogen receptor variant polypeptide (e.g., an androgen receptorvariant, for example AR-V1, AR-V2, AR-V3, AR-V4, AR-V5, AR-V6, AR-V7,AR-V8 or fragments thereof). For example, immunoassays may be used todetect or monitor the expression of at least one of the polypeptides ofthe invention in an organism. Polyclonal or monoclonal antibodies(produced as described above) that are capable of binding to such apolypeptide may be used in any standard immunoassay format (e.g., ELISA,Western blot, or RIA assay) to measure the level of the polypeptide. Insome embodiments, a compound that promotes a decrease in the expressionor biological activity of the polypeptide is considered particularlyuseful. Again, such a molecule may be used, for example, as atherapeutic to delay, ameliorate, or treat a androgen related disease ordisorder, e.g. prostate cancer in a human patient.

In another embodiment, a nucleic acid described herein (e.g., anandrogen receptor variant nucleic acid) is expressed as atranscriptional or translational fusion with a detectable reporter, andexpressed in an isolated cell (e.g., mammalian or insect cell) under thecontrol of a heterologous promoter, such as an inducible promoter. Thecell expressing the fusion protein is then contacted with a candidatecompound, and the expression of the detectable reporter in that cell iscompared to the expression of the detectable reporter in an untreatedcontrol cell. A candidate compound that alters the expression of thedetectable reporter is a compound that is useful for the treatment of aandrogen related disease or disorder, e.g. prostate cancer. In oneembodiment, the compound decreases the expression of the reporter.

Each of the DNA sequences listed herein may also be used in thediscovery and development of a therapeutic compound for the treatment ofandrogen related disease or disorder, e.g. prostate cancer. The encodedprotein, upon expression, can be used as a target for the screening ofdrugs. Additionally, the DNA sequences encoding the amino terminalregions of the encoded protein or Shine-Delgarno or other translationfacilitating sequences of the respective mRNA can be used to constructsequences that promote the expression of the coding sequence ofinterest. Such sequences may be isolated by standard techniques (Ausubelet al., supra).

The invention also includes novel compounds identified by theabove-described screening assays. Optionally, such compounds arecharacterized in one or more appropriate animal models to determine theefficacy of the compound for the treatment of a androgen related diseaseor disorder, e.g. prostate cancer. Desirably, characterization in ananimal model can also be used to determine the toxicity, side effects,or mechanism of action of treatment with such a compound. Furthermore,novel compounds identified in any of the above-described screeningassays may be used for the treatment of a androgen related disease ordisorder, e.g. prostate cancer in a subject. Such compounds are usefulalone or in combination with other conventional therapies known in theart.

Test Compounds and Extracts

In general, compounds capable of inhibiting the growth or proliferationof a androgen related disease or disorder, e.g. prostate cancer byaltering the expression or biological activity of an androgen receptorvariant polypeptide, variant, or fragment thereof are identified fromlarge libraries of either natural product or synthetic (orsemi-synthetic) extracts or chemical libraries according to methodsknown in the art. Numerous methods are also available for generatingrandom or directed synthesis (e.g., semi-synthesis or total synthesis)of any number of chemical compounds, including, but not limited to,saccharide-, lipid-, peptide-, and nucleic acid-based compounds.Synthetic compound libraries are commercially available from BrandonAssociates (Merrimack, N.H.) and Aldrich Chemical (Milwaukee, Wis.).Alternatively, libraries of natural compounds in the form of bacterial,fungal, plant, and animal extracts are commercially available from anumber of sources, including Biotics (Sussex, UK), Xenova (Slough, UK),Harbor Branch Oceangraphics Institute (Ft. Pierce, Fla.), and PharmaMar,U.S.A. (Cambridge, Mass.).

In one embodiment, test compounds of the invention are present in anycombinatorial library known in the art, including: biological libraries;peptoid libraries (libraries of molecules having the functionalities ofpeptides, but with a novel, non-peptide backbone which are resistant toenzymatic degradation but which nevertheless remain bioactive; see,e.g., Zuckermann, R. N. et al., J. Med. Chem. 37:2678-85, 1994);spatially addressable parallel solid phase or solution phase libraries;synthetic library methods requiring deconvolution; the ‘one-beadone-compound’ library method; and synthetic library methods usingaffinity chromatography selection. The biological library and peptoidlibrary approaches are limited to peptide libraries, while the otherfour approaches are applicable to peptide, non-peptide oligomer or smallmolecule libraries of compounds (Lam, Anticancer Drug Des. 12:145,1997).

Examples of methods for the synthesis of molecular libraries can befound in the art, for example in: DeWitt et al., Proc. Natl. Acad. Sci.U.S.A. 90:6909, 1993; Erb et al., Proc. Natl. Acad. Sci. USA 91:11422,1994; Zuckermann et al., J. Med. Chem. 37:2678, 1994; Cho et al.,Science 261:1303, 1993; Carrell et al., Angew. Chem. Int. Ed. Engl.33:2059, 1994; Carell et al., Angew. Chem. Int. Ed. Engl. 33:2061, 1994;and Gallop et al., J. Med. Chem. 37:1233, 1994.

Libraries of compounds may be presented in solution (e.g., Houghten,Biotechniques 13:412-421, 1992), or on beads (Lam, Nature 354:82-84,1991), chips (Fodor, Nature 364:555-556, 1993), bacteria (Ladner, U.S.Pat. No. 5,223,409), spores (Ladner U.S. Pat. No. 5,223,409), plasmids(Cull et al., Proc Natl Acad Sci USA 89:1865-1869, 1992) or on phage(Scott and Smith, Science 249:386-390, 1990; Devlin, Science249:404-406, 1990; Cwirla et al. Proc. Natl. Acad. Sci. 87:6378-6382,1990; Felici, J. Mol. Biol. 222:301-310, 1991; Ladner supra.).

Those skilled in the field of drug discovery and development willunderstand that the precise source of a compound or test extract is notcritical to the screening procedure(s) of the invention. Accordingly,virtually any number of chemical extracts or compounds can be screenedusing the methods described herein. Examples of such extracts orcompounds include, but are not limited to, plant-, fungal-, prokaryotic-or animal-based extracts, fermentation broths, and synthetic compounds,as well as modification of existing compounds.

When a crude extract is found to alter the biological activity of anandrogen receptor variant polypeptide, variant, or fragment thereof,further fractionation of the positive lead extract is necessary toisolate chemical constituents responsible for the observed effect. Thus,the goal of the extraction, fractionation, and purification process isthe careful characterization and identification of a chemical entitywithin the crude extract having anti-neoplastic activity. Methods offractionation and purification of such heterogenous extracts are knownin the art. If desired, compounds shown to be useful agents for thetreatment of a neoplasm are chemically modified according to methodsknown in the art.

Methods of Assaying Androgen Receptor Variant Biological Activity

Therapeutics useful in the methods of the invention include, but are notlimited to, those that alter an androgen receptor variant biologicalactivity associated with, for example cell proliferation, cell survival,cell secretion, gene expression. For example, in the case of prostatecancer, neoplastic cell growth is not subject to the same regulatorymechanisms that govern the growth or proliferation of normal cells and,accordingly, compounds that reduce the growth or proliferation ofprostate cancer are useful for the treatment of prostate cancer. Methodsof assaying cell growth and proliferation are known in the art. See, forexample, Kittler et al. (Nature. 432 (7020):1036-40, 2004) and byMiyamoto et al. (Nature 416(6883):865-9, 2002). Assays for cellproliferation generally involve the measurement of DNA synthesis duringcell replication. In one embodiment, DNA synthesis is detected usinglabeled DNA precursors, such as ([³H]-Thymidine or5-bromo-2′-deoxyuridine [BrdU], which are added to cells (or animals)and then the incorporation of these precursors into genomic DNA duringthe S phase of the cell cycle (replication) is detected (Ruefli-Brasseet al., Science 302(5650):1581-4, 2003; Gu et al., Science 302(5644):445-9, 2003).

Assays for measuring cell viability are known in the art, and aredescribed, for example, by Crouch et al. (J. Immunol. Meth. 160, 81-8);Kangas et al. (Med. Biol. 62, 338-43, 1984); Lundin et al., (Meth.Enzymol. 133, 27-42, 1986); Petty et al. (Comparison of J. Biolum.Chemilum. 10, 29-34, 1995); and Cree et al. (AntiCancer Drugs 6:398-404, 1995). Cell viability can be assayed using a variety ofmethods, including MTT(3-(4,5-dimethylthiazolyl)-2,5-diphenyltetrazolium bromide) (Barltrop,Bioorg. & Med. Chem. Lett. 1: 611, 1991; Cory et al., Cancer Comm. 3,207-12, 1991; Paull J. Heterocyclic Chem. 25, 911, 1988). Assays forcell viability are also available commercially. These assays includeCELLTITER-GLO Luminescent Cell Viability Assay (Promega), which usesluciferase technology to detect ATP and quantify the health or number ofcells in culture, and the CellTiter-Glo Luminescent Cell ViabilityAssay, which is a lactate dehyrodgenase (LDH) cytotoxicity assay.

Assays for measuring cell apoptosis are known to the skilled artisan.Apoptotic cells are characterized by characteristic morphologicalchanges, including chromatin condensation, cell shrinkage and membraneblebbing, which can be clearly observed using light microscopy. Thebiochemical features of apoptosis include DNA fragmentation, proteincleavage at specific locations, increased mitochondrial membranepermeability, and the appearance of phosphatidylserine on the cellmembrane surface. Assays for apoptosis are known in the art. Exemplaryassays include TUNEL (Terminal deoxynucleotidyl

Transferase Biotin-dUTP Nick End Labeling) assays, caspase activity(specifically caspase-3) assays, and assays for fas-ligand and annexinV. Commercially available products for detecting apoptosis include, forexample, Apo-ONE® Homogeneous Caspase-3/7 Assay, FragEL TUNEL kit(ONCOGENE RESEARCH PRODUCTS, San Diego, Calif.), the ApoBrdU DNAFragmentation Assay (BIOVISION, Mountain View, Calif.), and the QuickApoptotic DNA Ladder Detection Kit (BIOVISION, Mountain View, Calif.).

Microarrays

The methods of the invention may also be used for microarray-basedassays that provide for the high-throughput analysis of biomarkers. Theandrogen receptor variant nucleic acid molecules or polypeptides of theinvention are useful as hybridizable array elements in such amicroarray. The array elements are organized in an ordered fashion suchthat each element is present at a specified location on the substrate.Useful substrate materials include membranes, composed of paper, nylonor other materials, filters, chips, glass slides, and other solidsupports. The ordered arrangement of the array elements allowshybridization patterns and intensities to be interpreted as expressionlevels of particular genes or proteins. Methods for making nucleic acidmicroarrays are known to the skilled artisan and are described, forexample, in U.S. Pat. No. 5,837,832, Lockhart, et al. (Nat. Biotech.14:1675-1680, 1996), and Schena, et al. (Proc. Natl. Acad. Sci.93:10614-10619, 1996), herein incorporated by reference. Methods formaking polypeptide microarrays are described, for example, by Ge(Nucleic Acids Res. 28:e3.i-e3.vii, 2000), MacBeath et al., (Science289:1760-1763, 2000), Zhu et al. (Nature Genet. 26:283-289), and in U.S.Pat. No. 6,436,665, hereby incorporated by reference.

Nucleic Acid Microarrays

To produce a nucleic acid microarray oligonucleotides may be synthesizedor bound to the surface of a substrate using a chemical couplingprocedure and an ink jet application apparatus, as described in PCTapplication WO95/251116 (Baldeschweiler et al.), incorporated herein byreference. Alternatively, a gridded array may be used to arrange andlink cDNA fragments or oligonucleotides to the surface of a substrateusing a vacuum system, thermal, UV, mechanical or chemical bondingprocedure.

A nucleic acid molecule (e.g. RNA or DNA) derived from a biologicalsample may be used to produce a hybridization probe as described herein.The biological samples are generally derived from a patient, preferablyas a bodily fluid (such as blood, cerebrospinal fluid, phlegm, saliva,or urine) or tissue sample (e.g. a tissue sample obtained by biopsy,e.g. prostate tissue). For some applications, cultured cells or othertissue preparations may be used. The mRNA is isolated according tostandard methods, and cDNA is produced and used as a template to makecomplementary RNA suitable for hybridization. Such methods are describedherein. The RNA is amplified in the presence of fluorescent nucleotides,and the labeled probes are then incubated with the microarray to allowthe probe sequence to hybridize to complementary oligonucleotides (e.g.,androgen receptor variant nucleic acid molecules) bound to themicroarray.

Incubation conditions are adjusted such that hybridization occurs withprecise complementary matches or with various degrees of lesscomplementarity depending on the degree of stringency employed. Forexample, stringent salt concentration will ordinarily be less than about750 mM NaCl and 75 mM trisodium citrate, preferably less than about 500mM NaCl and 50 mM trisodium citrate, and most preferably less than about250 mM NaCl and 25 mM trisodium citrate. Low stringency hybridizationcan be obtained in the absence of organic solvent, e.g., formamide,while high stringency hybridization can be obtained in the presence ofat least about 35% formamide, and most preferably at least about 50%formamide. Stringent temperature conditions will ordinarily includetemperatures of at least about 30° C., more preferably of at least about37° C., and most preferably of at least about 42° C. Varying additionalparameters, such as hybridization time, the concentration of detergent,e.g., sodium dodecyl sulfate (SDS), and the inclusion or exclusion ofcarrier DNA, are well known to those skilled in the art. Various levelsof stringency are accomplished by combining these various conditions asneeded. In one embodiment, hybridization will occur at 30° C. in 750 mMNaCl, 75 mM trisodium citrate, and 1% SDS. In another embodiment,hybridization will occur at 37° C. in 500 mM NaCl, 50 mM trisodiumcitrate, 1% SDS, 35% formamide, and 100 μg/ml denatured salmon sperm DNA(ssDNA). In yet another embodiment, hybridization will occur at 42° C.in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50% formamide, and 200μg/ml ssDNA. Useful variations on these conditions will be readilyapparent to those skilled in the art.

The removal of nonhybridized probes may be accomplished, for example, bywashing. The washing steps that follow hybridization can also vary instringency. Wash stringency conditions can be defined by saltconcentration and by temperature. As above, wash stringency can beincreased by decreasing salt concentration or by increasing temperature.For example, stringent salt concentration for the wash steps willpreferably be less than about 30 mM NaCl and 3 mM trisodium citrate, andmost preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate.Stringent temperature conditions for the wash steps will ordinarilyinclude a temperature of at least about 25° C., at least about 42° C.,or at least about 68° C. In one embodiment, wash steps will occur at 25°C. in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS. In anotherembodiment, wash steps will occur at 42° C. in 15 mM NaCl, 1.5 mMtrisodium citrate, and 0.1% SDS. In yet another embodiment, wash stepswill occur at 68° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1%SDS. Additional variations on these conditions will be readily apparentto those skilled in the art.

A detection system may be used to measure the absence, presence, andamount of hybridization for all of the distinct sequences simultaneously(e.g., Heller et al., Proc. Natl. Acad. Sci. 94:2150-2155, 1997).Preferably, a scanner is used to determine the levels and patterns offluorescence.

Protein Microarrays

Androgen receptor variant polypeptides (e.g., androgen receptor variant,for example AR-V1, AR-V2, AR-V3, AR-V4, AR-V5, AR-V6, AR-V7, orfragments thereof), such as those described herein, may also be analyzedusing protein microarrays. Such arrays are useful in high-throughputlow-cost screens to identify peptide or candidate compounds that bind apolypeptide of the invention, or fragment thereof. Typically, proteinmicroarrays feature a protein, or fragment thereof, bound to a solidsupport. Suitable solid supports include membranes (e.g., membranescomposed of nitrocellulose, paper, or other material), polymer-basedfilms (e.g., polystyrene), beads, or glass slides. For someapplications, androgen receptor variant polypeptides (e.g., androgenreceptor variant, for example AR-V1, AR-V2, AR-V3, AR V4, AR-V5, AR-V6,AR-V7, AR-V8 or fragments thereof) are spotted on a substrate using anyconvenient method known to the skilled artisan (e.g., by hand or byinkjet printer). Preferably, such methods retain the biological activityor function of the protein bound to the substrate (e.g., androgenreceptor variant antibody binding).

The protein microarray is hybridized with a detectable probe. Suchprobes can be polypeptide (e.g., an androgen receptor variant antibody),nucleic acid, or small molecules. For some applications, polypeptide andnucleic acid probes are derived from a biological sample taken from apatient, such as a bodily fluid (such as blood, urine, saliva, orphlegm); a homogenized tissue sample (e.g. a tissue sample obtained bybiopsy, e.g. from the prostate); or cultured cells (e.g., lymphocytes).Probes can also include antibodies, candidate peptides, nucleic acids,or small molecule compounds derived from a peptide, nucleic acid, orchemical library. Hybridization conditions (e.g., temperature, pH,protein concentration, and ionic strength) are optimized to promotespecific interactions. Such conditions are known to the skilled artisanand are described, for example, in Harlow, E. and Lane, D., UsingAntibodies: A Laboratory Manual. 1998, New York: Cold Spring HarborLaboratories. After removal of non-specific probes, specifically boundprobes are detected, for example, by fluorescence, enzyme activity(e.g., an enzyme-linked calorimetric assay), direct immunoassay,radiometric assay, or any other suitable detectable method known to theskilled artisan.

Detection of an increase in the amount of an androgen receptor variantpolypeptide (e.g., androgen receptor variant, for example AR-V1, AR-V2,AR-V3, AR-V4, AR-V5, AR-V6, AR-V7, AR-V8 or fragments thereof) or anandrogen receptor variant polynucleotide present in a patient sample isuseful as a diagnostic for the presence of a androgen related disease ordisorder, e.g. prostate cancer. Optionally, androgen receptor variantdetection may be combined with the detection of other biomarkers, wherethe presence or level of the biomarker is correlated with the presenceof a androgen related disease or disorder, e.g. prostate cancer.

Pharmaceutical Compositions

The present invention contemplates pharmaceutical preparationscomprising an androgen receptor variant protein, a polynucleotide thatencodes an androgen receptor variant protein, or an androgen receptorvariant inhibitory nucleic acid molecule (e.g., a polynucleotide thathybridizes to and interferes with the expression of an androgen receptorvariant polynucleotide), together with a pharmaceutically acceptablecarrier. Polynucleotides of the invention may be administered as part ofa pharmaceutical composition. The compositions should be sterile andcontain a therapeutically effective amount of the polypeptides ornucleic acid molecules in a unit of weight or volume suitable foradministration to a subject.

These compositions ordinarily will be stored in unit or multi-dosecontainers, for example, sealed ampoules or vials, as an aqueoussolution or as a lyophilized formulation for reconstitution. As anexample of a lyophilized formulation, 10 mL vials are filled with 5 mLof sterile-filtered 1% (w/v) aqueous androgen receptor variantpolynucleotide solution, such as an aqueous solution of androgenreceptor variant polynucleotide or polypeptide, and the resultingmixture can then be lyophilized. The infusion solution can be preparedby reconstituting the lyophilized material using sterileWater-for-Injection (WFI).

The androgen receptor variant polynucleotide, or polypeptide, or analogsmay be combined, optionally, with a pharmaceutically acceptableexcipient. The term “pharmaceutically-acceptable excipient” as usedherein means one or more compatible solid or liquid filler, diluents orencapsulating substances that are suitable for administration into ahuman. The term “carrier” denotes an organic or inorganic ingredient,natural or synthetic, with which the active ingredient is combined tofacilitate administration. The components of the pharmaceuticalcompositions also are capable of being co-mingled with the molecules ofthe present invention, and with each other, in a manner such that thereis no interaction that would substantially impair the desiredpharmaceutical efficacy.

The compositions can be administered in effective amounts. The effectiveamount will depend upon the mode of administration, the particularcondition being treated and the desired outcome. It may also depend uponthe stage of the condition, the age and physical condition of thesubject, the nature of concurrent therapy, if any, and like factors wellknown to the medical practitioner. For therapeutic applications, it isthat amount sufficient to achieve a medically desirable result.

With respect to a subject having an androgen related disease ordisorder, an effective amount is sufficient to stabilize, slow, orreduce the progression of the disease or disorder, for example theprogression of prostate cancer. Generally, doses of activepolynucleotide compositions of the present invention would be from about0.01 mg/kg per day to about 1000 mg/kg per day. It is expected thatdoses ranging from about 50 to about 2000 mg/kg will be suitable. Lowerdoses will result from certain forms of administration, such asintravenous administration. In the event that a response in a subject isinsufficient at the initial doses applied, higher doses (or effectivelyhigher doses by a different, more localized delivery route) may beemployed to the extent that patient tolerance permits. Multiple dosesper day are contemplated to achieve appropriate systemic levels of theandrogen receptor variant polynucleotide or polypeptide compositions ofthe present invention.

A variety of administration routes are available. The methods of theinvention, generally speaking, may be practiced using any mode ofadministration that is medically acceptable, meaning any mode thatproduces effective levels of the active compounds without causingclinically unacceptable adverse effects. Other modes of administrationinclude oral, rectal, topical, intraocular, buccal, intravaginal,intracisternal, intracerebroventricular, intratracheal, nasal,transdermal, within/on implants, e.g., fibers such as collagen, osmoticpumps, or grafts comprising appropriately transformed cells, etc., orparenteral routes. Other useful approaches are described in Otto, D. etal., J. Neurosci. Res. 22: 83-91 and in Otto, D. and Unsicker, K. J.Neurosci. 10: 1912-1921.

Combination Therapies

Compositions and methods of the invention may be used in combinationwith any conventional therapy known in the art. In one embodiment, anandrogen receptor variant polynucleotide or polypeptide composition ofthe invention having anti-neoplastic activity may be used in combinationwith any anti-neoplastic therapy known in the art. Exemplaryanti-neoplastic therapies include, for example, chemotherapy,cryotherapy, hormone therapy, radiotherapy, and surgery. A androgenreceptor variant polynucleotide composition of the invention may, ifdesired, include one or more chemotherapeutics typically used in thetreatment of a neoplasm, such as abiraterone acetate, altretamine,anhydrovinblastine, auristatin, bexarotene, bicalutamide, BMS184476,2,3,4,5,6-pentafluoro-N-(3-fluoro-4-methoxyphenyl)benzene sulfonamide,bleomycin,N,N-dimethyl-L-valyl-L-valyl-N-methyl-L-valyl-L-proly-1-Lproline-t-butylamide,cachectin, cemadotin, chlorambucil, cyclophosphamide,3′,4′-didehydro-4′-deoxy-8′-norvin-caleukoblastine, docetaxol,doxetaxel, cyclophosphamide, carboplatin, carmustine (BCNU), cisplatin,cryptophycin, cyclophosphamide, cytarabine, dacarbazine (DTIC),dactinomycin, daunorubicin, dolastatin, doxorubicin (adriamycin),etoposide, 5-fluorouracil, finasteride, flutamide, hydroxyurea andhydroxyureataxanes, ifosfamide, liarozole, lonidamine, lomustine (CCNU),mechlorethamine (nitrogen mustard), melphalan, mivobulin isethionate,rhizoxin, sertenef, streptozocin, mitomycin, methotrexate,5-fluorouracil, nilutamide, onapristone, paclitaxel, prednimustine,procarbazine, RPR109881, stramustine phosphate, tamoxifen, tasonermin,taxol, tretinoin, vinblastine, vincristine, vindesine sulfate, andvinflunine Other examples of chemotherapeutic agents can be found inCancer Principles and Practice of Oncology by V. T. Devita and S.Hellman (editors), 6th edition (Feb. 15, 2001), Lippincott Williams &Wilkins Publishers.

The following examples are offered by way of illustration, not by way oflimitation. While specific examples have been provided, the abovedescription is illustrative and not restrictive. Any one or more of thefeatures of the previously described embodiments can be combined in anymanner with one or more features of any other embodiments in the presentinvention. Furthermore, many variations of the invention will becomeapparent to those skilled in the art upon review of the specification.The scope of the invention should, therefore, be determined not withreference to the above description, but instead should be determinedwith reference to the appended claims along with their full scope ofequivalents.

EXAMPLES

Studies described herein focus in part on AR-V7, one of the variantswith the most abundant expression and also the highest activity. Thestudies reported here show that AR-V7 was elevated by approximately20-fold in castration-resistant prostate cancer cells derived frompatients who died from metastatic prostate cancer following hormonetherapy failure. Interestingly, generally lower but varied AR-V7expression was also detected in prostate cancers that had not beeninfluenced by hormone ablation, and higher AR-V7 expression predictedPSA recurrence following local therapy in these patients. These resultssuggest that castration-resistant prostate cancer cells bearing thesignatory marker of a constitutively active AR are present prior tohormone therapies, and these cells may propagate under the selectionpressure induced by lack of sufficient androgens, leading to progressivecastration-resistant prostate cancer.

The results shown herein are particularly useful in methods ofdetermining if a subject with prostate cancer will respond to androgentherapy, where the level of expression or biological activity of anandrogen receptor variant polypeptide or the level of expression of anandrogen receptor variant nucleic acid is determined, and an alterationin the level of expression or biological activity relative to theexpression or biological activity in a reference indicates that thesubject will respond to androgen therapy. In certain cases, the methodcan be used to determine the prognosis of a prostate cancer subject inclinical remission.

The decoding and characterization of novel AR variants make it possibleto detect and manipulate prostate cancer cells with constitutivelyactive AR signaling under complete hormone ablation. Future studies willaddress the relative importance and clinical relevance ofligand-dependent versus ligand-independent routes toward hormone therapyfailure and focus on the development of methods and approaches to detectand modify the ligand-independent AR-signaling pathway.

Example 1 Identification of Cryptic AR Exons

BLAST searches were performed of the ˜170-kb AR intron sequences againstthe National Center for Biotechnology Information human expressedsequence tag database. High quality hits (99% identity) were found inintron 1 (6 hits), intron 2 (3 hits), and intron 3 (3 hits) but not inthe remaining four introns (See Table 1, below). Table 1 shows a summaryof transcribed genomic fragments within human AR gene introns.

TABLE 1 Intron Accession ID Size (bp) Identity Start* End** 1 AA886614231 99.6% 66722674 66722904 1 AA577938 293 99.0% 66723711 66724004 1AW5973726 294 100.0% 66723711 66724004 1 R89771 382 100.0% 6672543066725814 1 AI827337 490 100.0% 66750976 66751465 1 AW028775 437 99.8%66772546 66772983 2 BF327858 202 99.6% 66791497 66791698 2 BE007634 45099.6% 66791497 66791950 2 BE006793 355 100.0% 66819126 66819482 3CV379421 270 100.0% 66826610 66826880 3 CN283227 674 99.3% 6682941266830085 3 BF846156 538 99.7% 66831722 66832259 4 None 5 None 6 None 7None *Starting position coordinates on human chromosome X according toReference Human Genome Assembly (March 2006 release, HG18) **Endingposition coordinates on human chromosome X according to Reference HumanGenome Assembly (March 2006 release, HG18)

These transcribed “intronic” genomic fragments, considered as putativecryptic exons, were not spliced as currently annotated, and therefore,their exon-intron junctions were undefined. Because a functional ARwould most likely retain the AR DBD encoded by exons 2 and 3, threeputative cryptic exons in intron 3 were the focus in these studies inorder to determine whether and how they were joined (i.e., spliced) withthe upstream exon 3, and their potential to disrupt the AR open readingframe (ORF). Primers (P1, P2, and P3; Table 2, shown below) weredesigned to amplify and sequence mRNA transcripts containing exonsencoding AR DBD and the putative cryptic exons. Table 2 shows the primersets used in the study and the corresponding amplicon data.

TABLE 2 Amplified Primer Transcript Sets Forward Primer Reverse PrimerSize (bp) P1 TGTCACTATGGAGCTCTCA CACCTCTCAAATATGCTAGACGAATCTGTAR-V1: 842 (FIG. 1A) CATGTGG AR-V2: 959 AR-V3: 1126 AR-V4: 1243 P2TGTCACTATGGAGCTCTCA GTACTCATTCAAGTATCAGATATGCGGTA AR-V5: 888 (FIG. 1A)CATGTGG TCAT AR-V6: 968 P3 TGTCACTATGGAGCTCTCACTGTGGATCAGCTACTACCTTCAGCTC AR V7: 834 (FIG. 1A) CATGTGG P4GTTGCTCCCGCAAGTTTCC CTGTTGTGGATGAGCAGCTGAGAGTCT AR-V1 full- (FIG. 1C)TTCTC length ORF: 2134 P5 GTTGCTCCCGCAAGTTTCC TTTGAATGAGGCAAGTCAGCCTTTCTAR-V7 full- (FIG. 1C) TTCTC length ORF: 2113 P6 CCATCTTGTCGTCTTCGGACTGTTGTGGATGAGCAGCTGAGAGTCT AR-V1: 145 (FIG. 2A) AATGTTATGAAGC P7CCATCTTGTCGTCTTCGGA TTTGAATGAGGCAAGTCAGCCTTTCT AR-V7: 125 (FIG. 2A)AATGTTATGAAGC P8 CCATCTTGTCGTCTTCGGA AGCTTCTGGGTTGTCTCCTCAGTGG AR(FIG. 2A) AATGTTATGAAGC prototype: 143 SF3A3 TACGAAAGGAGGAGCTCAAGATCTCATTTGGGTGCTTCCGGT SF3A3: 107 (FIG. 2A) ATGCAA

All primers, forward and reverse (corresponding to the complementarystrand), are shown in the 5′ to 3′ direction.

Primer set 1 (P1) corresponds to (SEQ ID NO: 15)TGTCACTATGGAGCTCTCACATGTGG and (SEQ ID NO: 16)CACCTCTCAAATATGCTAGACGAATCTGT. Primer set 2 (P2) corresponds to(SEQ ID NO: 17) TGTCACTATGGAGCTCTCACATGTGG and (SEQ ID NO: 18)GTACTCATTCAAGTATCAGATATGCGGTATCAT. Primer set 3 (P3) corresponds to(SEQ ID NO: 19) TGTCACTATGGAGCTCTCACATGTGG and (SEQ ID NO: 20)CTGTGGATCAGCTACTACCTTCAGCTC. Primer set 4 (P4) corresponds to(SEQ ID NO: 21) GTTGCTCCCGCAAGTTTCCTTCTC and (SEQ ID NO: 22)CTGTTGTGGATGAGCAGCTGAGAGTCT. Primer set 5 (P5) corresponds to(SEQ ID NO: 23) GTTGCTCCCGCAAGTTTCCTTCTC and (SEQ ID NO: 24)TTTGAATGAGGCAAGTCAGCCTTTCT. Primer set 6 (P6) corresponds to(SEQ ID NO: 25) CCATCTTGTCGTCTTCGGAAATGTTATGAAGC and (SEQ ID NO: 26)CTGTTGTGGATGAGCAGCTGAGAGTCT. Primer set 7 (P7) corresponds to(SEQ ID NO: 27) CCATCTTGTCGTCTTCGGAAATGTTATGAAGC and (SEQ ID NO: 28)TTTGAATGAGGCAAGTCAGCCTTTCT. Primer set 8 (P8) corresponds to(SEQ ID NO: 29) CCATCTTGTCGTCTTCGGAAATGTTATGAAGC and (SEQ ID NO: 30)AGCTTCTGGGTTGTCTCCTCAGTGG. Primer set SF3A3 corresponds to(SEQ ID NO: 31) TACGAAAGGAGGAGCTCAATGCAA and (SEQ ID NO: 32)AGATCTCATTTGGGTGCTTCCGGT. Primer set 9 (P9) corresponds to(SEQ ID NO: 37) Tgtcactatggagctctcacatgtgg- and (SEQ ID NO: 38)Cattgtggccaacatgacacttca.

The detection and subsequent sequencing of the amplicons derived fromthe CWR22Rv1 cells confirmed that all three cryptic exons (CE1, CE2, andCE3) were joined with exon 3 (FIG. 1A). These sequencing results wereused to construct seven AR transcript variants, named AR-V 1 to AR-V7,each containing one of the three original cryptic exons (FIG. 1A).Analysis of transcripts containing cryptic exon 1 (CE1) also uncoveredan additional cryptic exon in intron 2, named CE4 (FIG. 1A), which wasspliced in both AR-V3 and AR-V4 (FIG. 1A). The genomic position of CE4is identical to the novel exon recently published by Dehm and colleagues(9), but the specific sequence reported differed from the consensussequences that were detected in the two CE4-containing variants (AR-V3and AR-V4; FIG. 1A). CWR22Rv1 is a human PCa cell line derived from aserially transplanted PCa xenograft that relapsed aftercastration-induced regression and is known to have a unique duplicatedexon 3 (13). The duplicated exon 3 was reflected in AR-V2 and AR-V4transcripts (FIG. 1A). AR-V5 and AR-V6 contained cryptic exon 2 (CE2)and differed by a contiguous 80-bp sequence at the 5′ junction of CE2due to alternative 5′ splicing sites spaced 80 by apart in CE2 (data notshown). Of importance, all seven AR variants harbor prematuretermination codons (PTC) downstream of AR DBD, generating ARLBD-truncated AR proteins if translated (FIG. 1A).

In preferred examples P9 is used to amplify AR-V8.

Example 2 Cloning of the Full-Length ORFs of AR-V1 and AR-V7

Semiquantitative RT-PCR analysis in a small set of clinical specimensdetected the variant transcripts prevalently in HRPC samples (FIG. 1B).The full-length ORFs of AR-V1 and AR-V7 were then amplified from twoclinical HRPC specimens and CWR22Rv1 cells (FIG. 1C). Sequence analysisof the full-length amplicons confirmed the intact ORF of AR NTD and DBDand, thus, the transcript structure for AR-V 1 and AR-V7. Due to theirrelative lower abundance (FIG. 1B), AR-V5 and AR-V6 were not furtherpursued for full-length ORF cloning. AR-V2 and AR-V4 were specific toCWR22Rv1 (data not shown) due to the presence of exon 3 duplication andtherefore also not pursued further. AR-V3 harbors a stop codon in CE4and would lack the second zinc finger of AR DBD encoded by exon 3. Suchvariants may not be functional according to a previous study (14),although the study by Dehm and colleagues (9) suggested otherwise. Inaddition, the full-length ORF for AR-V3 thus far has not been detectedin sequenced clones (data not shown). For these reasons, only AR-V 1 andAR-V7 were pursued further.

Example 3 Expression Analysis of AR-V1 and AR-V7

HRPC specimens expressed consistently higher levels of AR-V1, AR-V7, andthe prototype AR detected using optimized primer sets specific to eachtarget transcript (FIG. 2A). Expression of the prototype AR can bereadily detected at 28 PCR cycles, whereas detection of the AR ARvariants, at mRNA levels, relative to the prototype AR (FIG. 2A).Quantitative real-time RT-PCR of AR-V1, AR-V7, and prototype AR wasperformed on an expanded series of human prostate tissues (n=124) andcell lines (n=9; see FIG. 5). Expression levels of AR-V1, AR-V7, andprototype AR were significantly higher in HRPC (n=25) than inhormone-naive PCa (n=82; P<0.0001, Mann-Whitney test). Adjusted foramplification efficiency, the average expression values for prototype AR(see FIG. 6A), AR-V 1 (see FIG. 6B), and AR-V7 (FIG. 2B) were elevatedby 11-, 22-, and 20-fold, respectively, when compared with hormone-naivePCa. It is unlikely that nuclear splicing intermediates of the prototypeAR gene contributed to the detected AR variant signals because nRNAcontributed <5% of the signal when compared with cytoplasmic RNA on aper cell basis (see FIG. 7). A subset of hormone-naive PCa expressed ARvariants at levels comparable with those in HRPC specimens (FIG. 2B).This elevated AR-V7 expression was associated with worse clinicaloutcome (log-rank P=0.012), as defined by prostate-specific antigen(PSA) recurrence following surgical treatment (FIG. 2C), in 66 RRP casesfor which long-term clinical follow-up data were available. In this samesample set (n=66), higher prototype AR mRNA levels did not predict PSAfailure (see FIG. 8A). Similarly, higher ratio of V7/AR did not predictPSA failure (see FIG. 8B), although there seemed to be a trend. AR-V 1expression was not associated with this clinical outcome (log-rankP=0.498; data not shown). It is unknown why AR-V 1 and AR-V7, althoughboth overexpressed in HRPC specimens, differed in their association withPSA recurrence. It is worth noting that our preliminary analysispredicted that AR-V 1 variant-specific sequences (FIG. 1A) lack thebasic amino acids characteristic of the bipartite nuclear localizingsequence (15) and therefore may not be a fully functional nuclearreceptor (data not shown).

Table 3, shown below, shows androgen therapies and the metastatic sitesof the assayed HPRC cases.

TABLE 3 Gleason Score at A# Dx Androgen-targeted therapies Assayed Mets 2 7 leuprolide, Flutamide, Liver  7 9 leuprolide, Flutamide, Subdural 8 6 goserelin, Flutamide Liver  9 7 leuprolide, flutamide Periportal LN10 8 goserelin, flutamide Perigastric LN 16 7 leuprolide, flutamideAdrenal 17 7 leuprolide, flutamide Hilar LN 19** 8 leuprolide, flutamidePelvic LN 19** 8 leuprolide, flutamide Bone (Humerus) 21 7 leuprolide,flutamide Iliac crest soft tissue 23 7 goserelin Liver 24 6 leuprolide,flutamide Pericardial Met 26 8 goserelin, flutamide Bone (T12) 27 7leuprolide, flutamide Axillary LN 28 7 leuprolide, flutamide, AnteriorMediastinal LN orchiectomy 29 6 goserelin, flutamide Inguinal LN 30 7leuprolide, flutamide Liver 31 6 goserelin, flutamide Subdural 32 8orchiectomy Bone (Rib) 33 7 orchiectomy Subdural 34 5 leuprolide,flutamide Liver *A total of 21 sectioned, pathologically andanatomically validated metastatic hormone refractory prostate cancerlesions derived from 20 autopsy cases were prepared and assayed. **Twodistant mets from case number 19 were assayed.

Example 4 AR-V7 is Translated and Constitutively Active

Transcript variants harboring PTC may be subjected to nonsense-mediateddecay (16). Indeed, although similar transcript variants have beenpreviously characterized for other steroid hormone receptor familymembers (17), no corresponding protein product has been reliably shown.Using the unique peptide sequence encoded by AR CE3, polyclonalantibodies were generated specifically against AR-V7. The antibodiesrecognized a single band of expected size (80 kDa) in VCaP and CWR22Rv1cells (FIG. 3A), which expressed highest levels of AR-V7 mRNA (FIG. 5).Similarly, AR-V7 protein was detected in protein extracts from these twocell lines that were enriched for AR proteins by IP with an antibodyagainst the AR NTD (FIG. 3B). In addition, the antibody detected theAR-V7 antigen in two clinical HRPC specimens using both whole tissuelysates and IP concentrated extracts (FIG. 3C). Moreover, using IPconcentrated protein extracts, AR-V7 protein expression was detected in10 of 14 human PCa xenografts, 12 of which were derived from HRPCpatients (18), but in only 1 of the 9 hormone-naive radicalprostatectomy specimens (FIG. 9). In CWR22Rv1 cells, small interferingRNA-mediated knockdown of AR-V7 expression or depletion of AR-V7 usinganti-AR-V7 both resulted in significant reduction of the commonlyobserved f 80-kDa protein band but did not affect prototype ARexpression (FIG. 10), suggesting nearly equivalent AR-V7 and prototypeAR protein levels in this cell line. Although the prototype AR respondedto the treatment of androgen by localizing to the nucleus, a largefraction of endogenous AR-V7 was localized in the nucleus in the absenceof androgen and the proportion of nuclear AR-V7 did not change onandrogen stimulation (FIG. 3D). The putative functional role of AR-V7was investigated using exogenously transfected AR-V7 in AR-negative PC-3cells. AR-V7 localized to the nucleus (FIG. 4A) and induced PSA reportergene expression in an androgen-independent manner (FIG. 4B).Furthermore, in androgen-responsive LNCaP cells AR-V7 induced canonicalandrogen-responsive genes, such as KLK3, KLK2, NKX3-1, FKBP5, andTMPRSS2, in the absence of androgens, as shown by global gene expressionanalysis following transfection of the exogenous AR-V7 cDNA in LNCaPcells (FIG. 4C).

Hormonal therapy for advanced PCa is most commonly achieved byorchiectomy, systemic administration of LHRH agonists (e.g.,leuprolide), and/or antiandrogens (e.g., bicalutamide). There aresignificant drawbacks associated with all existing androgen manipulationapproaches. First, a variable period of clinical regression is followedby progression to HRPC, a lethal manifestation of the disease that isresistant to further therapies (4). Second, there are debilitatingconsequences from these treatments that must be considered when decidingwhether and when to commence hormone therapy (2). Furthermore,sufficient levels of local androgens continue to be present in patientstreated with combined androgen blockade (19). In spite of thesechallenges, hormone therapies remain the mainstay of treatment forpatients with advanced PCa primarily due to the often dramatic clinicalresponses. The discovery of multiple LBD-truncated AR variants thatmediate androgen-independent AR functions in HRPC and a subset ofadvanced but hormone-naive PCa adds another level of detail to thecomplex molecular mechanisms underlying the development of HRPC and maysuggest new diagnostic and therapeutic approaches targeting this lethaldisease. Indeed, these findings reinforce arguments for specifictargeting of the AR NTD to achieve complete abrogation of AR signaling(20). Our quantitative mRNA data suggested that AR-V7 is a low-abundancevariant relative to the prototype AR in the vast majority of clinicalspecimens, including HRPC (FIG. 11). The relative contribution of theprototype AR and the less abundant yet androgen-independent AR variantsto the development of HRPC is currently unknown and will requiredetailed investigation. Nevertheless, the detection of such variants inproper target tissues or cells, on further refinement of the detectionmethods, may predict or monitor hormone therapy efficacy and couldpotentially help guide the decision-making process about the type andtiming of therapies given to patients with advanced PCa.

Example 5 Development and Testing of the AR-V7 Monoclonal Antibody

It has been shown that AR-V7 is elevated by 20 fold following hormonetherapy failure, and higher AR-V7 levels predict PSA recurrence (Hu etal. Cancer Research 69(1):16-22, 2009). However, these findings werebased on mRNA levels. In a clinical setting, determination of mRNAlevels can be difficult. In addition, although polyclonal antibodieshave been generated (Hu et al. Cancer Research 69(1):16-22, 2009), thepolyclonal antibodies only worked for western blot andimmunoprecipitation. The results described herein describe experimentsfocused on generating monoclonal antibodies against AR-V7. The resultsshown in FIGS. 12-19 demonstrate that clone 2D12 is highly specific forAR-V7, that 2D12 works in western blot, immunofluorescence, andimmunohistochemistry. The availability of 2D12 made it possible todetect the antigen a clinically relevant setting. Diagnostic andprognostic assays using this antibody are to be developed and validatedin prospective clinical trials.

Example 6 Discovery of AR-V8 Using Tiling Expression Microarray

The in silico based methods described above relied on depositedsequences in the public domain in the discovery phase, therefore are notcomprehensive. It is possible that we had only captured a fraction ofthe AR variants. This incomplete profile of AR variant could limit thechoices for biomarker validation and therapeutic development. To addressthese limitations, we interrogated the entire human androgen receptorgene and the immediate vicinity, ˜200 kb in length, using genomic tilingarrays. This comprehensive approach, so far performed in two samples(CWR22Rv1 and TURP2), confirmed some of the previously characterized ARvariants, and discovered a novel AR variant, AR-V8, that is abundantlyexpressed based on the overall signal intensity shown in FIG. 20. Thesplicing junctions for AR-V8 has been defined and variant specificnucleotide sequence has been validated (SEQ ID NO: 39) and the variantspecific peptide sequence similarly deduced (SEQ ID NO: 40).

Materials and Methods

The Examples described herein were performed using, but not limited to,the following materials and methods.

Human Prostate Tissue Samples

Hormone-naive prostate tissue specimens used in this study (n=82) werecollected and fresh frozen at the time of radical retropubicprostatectomy (RRP), from 1993 to 2001, at the Johns Hopkins Hospital.Prostate specimens were processed as described previously before RNAextraction (10). HRPC specimens were either collected at the time of thetransurethral resection of the prostate (TURP) operation in patients whofailed hormone therapies (n=4) or metastatic HRPC tissues (n=21)collected from 20 patients who died from PCa, as part of the JohnsHopkins Autopsy Study of lethal PCa (Supplementary Table 51; ref 11).The use of surgical and autopsy specimens for molecular analysis wasapproved by the Johns Hopkins Medicine Institutional Review Boards.

Cloning and Sequencing of AR Variants

First-strand cDNA synthesis was performed using 500 ng total RNA, 0.5 Agoligo(dT), and 200 units of SuperScript II reverse transcriptase(Invitrogen) in a volume of 20 AL. PCR products derived from the primerpairs (Supplementary Table S2) were cloned into TopoTA vector(Invitrogen) and subjected to sequencing analysis using the AppliedBiosystems 3730×1 DNA analyzer. To facilitate the amplification andsequencing of GC-rich AR NTD, DMSO (10%) was added in the PCR forfull-length variant cloning and subsequent sequencing analysis.

AR Variant mRNA Expression Analysis

For semiquantitative reverse transcription-PCR (RT-PCR) analysis, 2.5%of the cDNA product from 500 ng input total RNA was used for each sampleand each transcript. For real-time quantitative RT-PCR, 0.125% of thecDNA product was used in the iQ SYBR Green Supermix assays (Bio-Rad).Given the highly variable expression of many genes among clinicalspecimens, we analyzed previously published expression microarray dataand identified SF3A3, which encodes a splicing factor, as a referencegene for normalization due to its stable expression levels among variousprostate specimens, including HRPC, primary PCa, normal prostatesamples, and cell lines (12). Only primer pairs with validatedamplification specificity were used (Supplementary Table S2). Followingvalidation of equal amplification efficiencies for both targettranscripts and SF3A3, the average threshold cycle (Ct) numbers fromreactions run in triplicate were used for comparative thresholdanalysis. For presentation purposes and for comparison among differentfigures, all expression values were log 2 transformed with measurablevalues for the RRP cases centered at zero.

AR Variant Protein Analysis

Whole-cell lysates were prepared using radioimmunoprecipitation assaybuffer (Pierce) according to the vendor's recommendations. Nuclear andcytosolic extracts were prepared using the Nuclear and CytoplasmicExtraction Reagents (Pierce). Protein samples were resolved on 4% to 12%gradient SDS-PAGE gels and subjected to standard immunoblot analysiswith anti-AR(N20) (Santa Cruz Biotechnology), anti-AR-V7, oranti-beta-actin (Sigma-Aldrich) antibodies. The mouse polyclonalanti-AR-V7 antibody was developed using the COOH-terminal peptide(CKHLKMTRP) specific to the AR-V7 protein by a commercial vendor (A&GPharmaceutical). For immunoprecipitation (IP), a total of 300 μg inputwhole-cell lysates from cell lines or human tissues was precipitatedwith 4 μg of monoclonal anti-AR(441) (Santa Cruz Biotechnology) orcontrol mouse IgG, followed by the addition of protein G-agarose (GEHealthcare), and subjected to standard immunoblot analysis.

Luciferase Reporter Assay

pEGFP-AR and pEGFP-Q640X, which contain the full-length prototype AR andAR Q640X LBD-truncated mutant cDNA, were kind gifts of Dr. JocelynCéraline (Université Strasbourg, Strasbourg, France). The cDNA encodingthe full-length AR-V7 was inserted into the pEGFP-C3 vector to expressthe GFP-AR-V7 fusion protein. Each of these constructs was cotransfectedtogether with the PSAP1 luciferase reporter plasmid and pRL-CMV plasmid,an internal Renila luciferase transfection control. Transfected cellswere cultured in phenol red-free RPMI 1640 containing 10%charcoal-stripped serum (CSS) for 24 h and cultured for another 24 h inthe presence or absence of R1881 (NEN) before being harvested andsubjected to the Dual-Luciferase Reporter Assay (Promega).

Tiling Array Analysis

Tiling expression microarrays were designed to cover a 200 kb intervalof the X chromosome (chrX:66,680,000-66,880,000) encompassing the entirehuman AR gene and the immediate vicinity, at 50 bp spacing with 10 bpoverlap. Probes from both sense and antisense strands were included.Probes with repetitive elements and multiple hits in the human genomewere excluded. The genomic sequences in FASTA text format were loaded tothe Agilent eArray server under the simple tiling tab and processed forthe manufacturing of this custom array. The routine labeling methodinvolves incorporation of aminoallyl-dUTP during cDNA synthesis followedby coupling with monofunctional NHS-CyeS. The labeled products wouldhybridize against probes corresponding to the sense strand DNA. Thismethod requires at least 20 μg of input RNA and is often limited by thelow labeling efficiency especially for target transcripts with long 3′untranslated region (UTR). In addition, all transcripts (not just AR)would be labeled, increasing the likelihood of non-specifichybridization. The described method takes advantage of known distancebetween exon 1 and the start of cryptic exons. A modified T7 Eberwineprimer with the core T7 promoter was used in second strand cDNAsynthesis. Following an additional round of polyT primed DNA synthesis,double strand DNA templates with 5′ binding sites for standard RNAlinear amplification were generated. These labeled sense RNA willhybridize with antisense probes on the tiling array. The tiling arraydata was viewed with the Affymetrix Integrated Genome Browser.

Statistical Analysis

All data were analyzed using Stata v10.0 statistical analyses software(Stata Corp.). The Mann-Whitney test was used to evaluate distributiondifference across two groups. Cox proportional hazard regression wasused to identify significant prognostic factors for prediction of PCaprogression-free survival. The proportional hazard assumption wasverified by examination of residual plots and Schoenfeld residuals. Logrank was used to test equality of survivor functions across two groups.Statistical significance in this study was set as P V 0.05.

The present invention has been described in detail, including thepreferred embodiments thereof. However, it will be appreciated thatthose skilled in the art, upon consideration of the present disclosure,may make modifications and/or improvements of this invention and stillbe within the scope and spirit of this invention as set forth in thefollowing claims.

All publications and patent documents cited in this application areincorporated by reference in their entirety for all purposes to the sameextent as if each individual publication or patent document were soindividually denoted. By their citation of various references in thisdocument, Applicants do not admit any particular reference is “priorart” to their invention.

The following specific references, also incorporated by reference, areindicated above by corresponding reference number.

-   1. Heinlein C A, Chang C. Androgen receptor in prostate cancer.    Endocr Rev 2004; 25:276-308.-   2. Gelmann E P. Molecular biology of the androgen receptor. J Clin    Oncol 2002; 20:3001-15.-   3. Shang Y, Myers M, Brown M. Formation of the androgen receptor    transcription complex. Mol Cell 2002; 9:601-10.-   4. Armstrong A J, Carducci M A. New drugs in prostate cancer. Curr    Opin Urol 2006; 16:138-45.-   5. Scher H I, Sawyers C L. Biology of progressive,    castration-resistant prostate cancer: directed therapies targeting    the androgen-receptor signaling axis. J Clin Oncol 2005; 23:8253-61.-   6. Agoulnik I U, Weigel N L. Androgen receptor action in    hormone-dependent and recurrent prostate cancer. J Cell Biochem    2006; 99:362-72.-   7. Céraline J, Cruchant M D, Erdmann E, et al. Constitutive    activation of the androgen receptor by a point mutation in the hinge    region: a new mechanism for androgen-independent growth in prostate    cancer. Int J Cancer 2004; 108:152.-   8. Libertini S J, Tepper C G, Rodriguez V, Asmuth D M, Kung H J,    Mudryj M. Evidence for calpain-mediated androgen receptor cleavage    as a mechanism for androgen independence. Cancer Res 2007;    67:9001-5.-   9. Dehm S M, Schmidt L J, Heemers H V, Vessella R L, Tindall D J.    Splicing of a novel androgen receptor exon generates a    constitutively active androgen receptor that mediates prostate    cancer therapy resistance. Cancer Res 2008; 68:5469-77.-   10. Luo J, Duggan D J, Chen Y, et al. Human prostate cancer and    benign prostatic hyperplasia: molecular dissection by gene    expression profiling. Cancer Res 2001; 61:4683-8.-   11. Suzuki H, Freije D, Nusskern D R, et al. Interfocal    heterogeneity of PTEN/MMAC1 gene alterations in multiple metastatic    prostate cancer tissues. Cancer Res 1998; 58:204-9.-   12. Dhanasekaran S M, Barrette T R, Ghosh D, et al. Delineation of    prognostic biomarkers in prostate cancer. Nature 2001; 412:822-6.-   13. Tepper C G, Boucher D L, Ryan P E, et al. Characterization of a    novel androgen receptor mutation in a relapsed CWR22 prostate cancer    xenograft and cell line. Cancer Res 2002; 62:6606-14.-   14. Quigley C A, Evans B A, Simental J A, et al. Complete androgen    insensitivity due to deletion of exon C of the androgen receptor    gene highlights the functional importance of the second zinc finger    of the androgen receptor in vivo. Mol Endocrinol 1992; 6:1103-12.-   15. Zhou Z X, Sar M, Simental J A, Lane M V, Wilson E M. A    ligand-dependent bipartite nuclear targeting signal in the human    androgen receptor. Requirement for the DNA-binding domain and    modulation by N H2-terminal and carboxyl-terminal sequences. J Biol    Chem 1994; 269:13115-23.-   16. Pan Q, Saltzman A L, Kim Y K, et al. Quantitative microarray    profiling provides evidence against widespread coupling of    alternative splicing with nonsense-mediated mRNA decay to control    gene expression. Genes Dev 2006; 20:153-8.-   17. Hirata S, Shoda T, Kato J, Hoshi K. Isoform/variant mRNAs for    sex steroid hormone receptors in humans. Trends Endocrinol Metab    2003; 14:124-9.-   18. Saramãki O R, Porkka K P, Vessella R L, Visakorpi T. Genetic    aberrations in prostate cancer by microarray analysis. IntJ Cancer    2006; 119:1322-9.-   19. Montgomery R B, Mostaghel E A, Vessella R, et al. Maintenance of    intratumoral androgens in metastatic prostate cancer: a mechanism    for castration-resistant tumor growth. Cancer Res 2008; 68:4447-54.-   20. Dehm S M, Tindall D J. Androgen receptor structural and    functional elements: role and regulation in prostate cancer Mol    Endocrinol 2007; 21:2855-63.-   21. Huggins C, Hodges C V. Studies on prostatic cancer: I. The    effect of castration, of estrogen and of androgen injection on serum    phosphatases in metastatic carcinoma of the prostate. 1941. J.    Uro1.168(1), 9-12 (2002).-   22. Maroni P D, Crawford E D. The benefits of early androgen    blockade. Best Pract. Res. Clin. Endocrinol. Metab. 22(2), 317-329    (2008).-   23. Fleming M T, Morris M J, Heller G, Scher H I. Post-therapy    changes in PSA as an outcome measure in prostate cancer clinical    trials. Nat. Clin. Pract. Oncol. 3(12), 658-667 (2006).-   24. Chen Y, Sawyers C L, Scher H I. Targeting the androgen receptor    pathway in prostate cancer. Curr. Opin. Pharmacol. 8(4), 440-448    (2008).-   25. Small E J, Ryan C J. The case for secondary hormonal therapies    in the chemotherapy age. J. Uro1.176(6 Pt 2), 566-571 (2006).-   26. Abrahamsson P A. Neuroendocrine cells in tumour growth of the    prostate. Endocr. Relat. Cancer 6(4), 503-519 (1999).-   27. Chen C D, Welsbie D S, Tran C et al. Molecular determinants of    resistance to antiandrogen therapy. Nat. Med. 10(1), 33-39 (2004).-   28. Linja M J, Visakorpi T. Alterations of androgen receptor in    prostate cancer. J. Steroid Biochem. Mol. Biol. 92(4), 255-264    (2004).-   29. Chmelar R, Buchanan G, Need E F, Tilley W, Greenberg N M.    Androgen receptor coregulators and their involvement in the    development and progression of prostate cancer. Int. J. Cancer    120(4), 719-733 (2007).-   30. Kaarbo M, Klokk T I, Saatcioglu F. Androgen signaling and its    interactions with other signaling pathways in prostate cancer.    Bioessays 29(12), 1227-1238 (2007).-   31. Mostaghel E A, Nelson P S. Intracrine androgen metabolism in    prostate cancer progression: mechanisms of castration resistance and    therapeutic implications. Best Pract. Res. Clin. Endocrinol. Metab.    22(2), 243-258 (2008).-   32. Hu R, Dunn T A, Wei S et al. Ligand-independent androgen    receptor variants derived from splicing of cryptic exons signify    hormone-refractory prostate cancer. Cancer Res. 69(1), 16-22 (2009).

What is claimed is:
 1. A method of detecting an androgen receptorvariant 7 (AR-V7) having a nucleic acid sequence comprising SEQ ID NO: 1or a fragment thereof, wherein the fragment comprises a portion ofcryptic exon 3, in a human patient suffering from prostate cancer, themethod comprising: a. obtaining a sample from the human patient, whereinthe sample comprises mRNA; b. contacting the sample with one or moreprimers or probes, wherein at least one of the primers or probesspecifically binds to the portion of cryptic exon 3 of the nucleic acidsequence comprising SEQ ID NO: 1 or the fragment thereof, and c.detecting the binding of the one or more primers or probes to theportion of cryptic exon 3 of the nucleic acid sequence comprising SEQ IDNO: 1 or a fragment thereof in the sample, thereby detecting AR-V7 inthe human patient suffering from prostate cancer.
 2. The method of claim1, wherein the nucleic acid sequence detected comprises SEQ ID NO:
 1. 3.The method of claim 1, wherein the step of detecting comprises detectingby nucleic acid amplification.
 4. The method of claim 1, wherein thestep of detecting comprises detecting by hybridization reaction.
 5. Themethod of claim 4, wherein the hybridization reaction further compriseshybridizing the sample to one or more primer sets.
 6. The method ofclaim 5, wherein the hybridization reaction is a polymerase chainreaction.
 7. The method of claim 6, wherein the polymerase chainreaction is reverse transcription polymerase chain reaction.
 8. Themethod of claim 1, wherein the step of detecting comprises detecting byexpressed sequence tags.
 9. The method of claim 1, wherein the step ofdetecting comprises detecting by microarray.
 10. The method of claim 1,wherein the step of detecting comprises detecting by localization. 11.The method of claim 1, wherein the sample is a biological sample. 12.The method of claim 11, wherein the biological sample is a selected fromthe group consisting of: prostate cancer tissue biopsy, fresh orarchival surgical specimens, circulating prostate tumor cells present inthe blood, serum, urine and cell lines; or combinations thereof.
 13. Themethod of claim 12, wherein the prostate cancer tissue biopsy is a tumorcell.
 14. The method of claim 13, wherein the tumor cell is a prostatecancer cell.
 15. The method of claim 1, wherein the prostate cancer ishormone naïve.
 16. The method of claim 11, wherein the biological sampleis a tumor sample previously treated with hormone therapy.
 17. Themethod of claim 11, wherein the biological sample is from prostate. 18.The method of claim 11, wherein the biological sample is from a patientundergoing treatment for prostate cancer.
 19. The method of claim 18,wherein the cancer is androgen refractory prostate cancer.
 20. Themethod of claim 1, wherein the patient is in remission from prostatecancer.
 21. The method of claim 1, wherein the expression level of SEQID NO: 1 or a fragment thereof is determined relative to that of SF3A3or GAPDH.
 22. The method of claim 1, further comprising after step a.and prior to step b. reverse transcribing the mRNA obtained in step a.to produce a cDNA product.
 23. The method of claim 1, wherein thedetection of the binding of the one or more primers or probes in step c.is performed by a reverse transcription polymerase chain reaction andwherein the sample is contacted by at least two primers, wherein atleast one primer binds to the portion of cryptic exon
 3. 24. The methodof claim 1, wherein the one or more primers are:CTGTGGATCAGCTACTACCTTCAGCTC (SEQ ID NO: 20); orTTTGAATGAGGCAAGTCAGCCTTTCT (SEQ ID NO: 24).
 25. The method of claim 1,wherein the one or more primers are a primer set selected from: (P3)(SEQ ID NO: 19) TGTCACTATGGAGCTCTCACATGTGG and (SEQ ID NO: 20)CTGTGGATCAGCTACTACCTTCAGCTC; (P5) (SEQ ID NO: 23)GTTGCTCCCGCAAGTTTCCTTCTC and (SEQ ID NO: 24) TTTGAATGAGGCAAGTCAGCCTTTCT;or (P7) (SEQ ID NO: 27) CCATCTTGTCGTCTTCGGAAATGTT ATGAAGC and(SEQ ID NO: 28) TTTGAATGAGGCAAGTCAGCCTTTCT.